6WN8

2.70 Angstrom Resolution Crystal Structure of Uracil Phosphoribosyl Transferase from Klebsiella pneumoniae

PDB DOI: https://doi.org/10.2210/pdb6WN8/pdb

Classification: TRANSFERASE
Organism(s): Klebsiella pneumoniae subsp. pneumoniae
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-04-22 Released: 2020-05-06
Deposition Author(s): Minasov, G., Shuvalova, L., Kiryukhina, O., Dubrovska, I., Satchell, K.J.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.219
R-Value Work: 0.189
R-Value Observed: 0.190

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Literature

A Structural Systems Biology Approach to High-Risk CG23 Klebsiella pneumoniae.

Inniss, N.L., Kochan, T.J., Minasov, G., Wawrzak, Z., Chang, C., Tan, K., Shuvalova, L., Kiryukhina, O., Pshenychnyi, S., Wu, R., Dubrovska, I., Babnigg, G., Endres, M., Anderson, W.F., Hauser, A.R., Joachimiak, A., Satchell, K.J.F.

(2023) Microbiol Resour Announc 12: e0101322-e0101322

PubMed: 36695589 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1128/mra.01013-22
Primary Citation of Related Structures:
6DT3, 6DUX, 6DVV, 6DXN, 6E85, 6NAU, 6NBG, 6NDI, 6WN5, 6WN8, 6X1L, 7RJJ, 7TL5, 7TZP

PubMed Abstract:
Klebsiella pneumoniae is a leading cause of antibiotic-resistant-associated deaths in the world. Here, we report the deposition of 14 structures of enzymes from both the core and accessory genomes of sequence type 23 (ST23) K1 hypervirulent K. pneumoniae.

Organizational Affiliation

Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA.

Macromolecule Content

Total Structure Weight: 239.47 kDa
Atom Count: 16,930
Modelled Residue Count: 2,087
Deposited Residue Count: 2,110
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uracil phosphoribosyltransferase	A, B, C, D, E A, B, C, D, E, F, G, H, I, J	211	Klebsiella pneumoniae subsp. pneumoniae	Mutation(s): 0 Gene Names: upp, C4Y86_021390, C4Z38_007125, E3U37_17930, E3U38_17635, E9161_15415, E9167_16225, EJ893_03135, FAT88_15980, NCTC9504_02023... upp, C4Y86_021390, C4Z38_007125, E3U37_17930, E3U38_17635, E9161_15415, E9167_16225, EJ893_03135, FAT88_15980, NCTC9504_02023, RJA_06790 EC: 2.4.2.9
UniProt
Find proteins for A6TCB0 (Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)) Explore A6TCB0 Go to UniProtKB: A6TCB0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A6TCB0
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose	K	2		N/A	Interactions Focus chain K Interactions & Density Focus chain K
Glycosylation Resources
GlyTouCan: G05551OP GlyCosmos: G05551OP

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BDF Query on BDF Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain JB [auth E] SDF format, chain KB [auth E] SDF format, chain L [auth A] SDF format, chain M [auth A] MOL2 format, chain AA [auth B] MOL2 format, chain JB [auth E] MOL2 format, chain KB [auth E] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A]	AA [auth B], JB [auth E], KB [auth E], L [auth A], M [auth A]	beta-D-fructopyranose C₆ H₁₂ O₆ LKDRXBCSQODPBY-ARQDHWQXSA-N		Interactions Focus chain AA [auth B] Focus chain JB [auth E] Focus chain KB [auth E] Focus chain L [auth A] Focus chain M [auth A] Interactions & Density Focus chain AA [auth B] Focus chain JB [auth E] Focus chain KB [auth E] Focus chain L [auth A] Focus chain M [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain AB [auth D] SDF format, chain AC [auth F] SDF format, chain AD [auth H] SDF format, chain BA [auth B] SDF format, chain BB [auth D] SDF format, chain BC [auth F] SDF format, chain BD [auth H] SDF format, chain CA [auth B] SDF format, chain CB [auth D] SDF format, chain CC [auth F] SDF format, chain CD [auth H] SDF format, chain DA [auth B] SDF format, chain DB [auth D] SDF format, chain DC [auth F] SDF format, chain DD [auth I] SDF format, chain EA [auth B] SDF format, chain EB [auth D] SDF format, chain ED [auth I] SDF format, chain FA [auth B] SDF format, chain FB [auth D] SDF format, chain FD [auth I] SDF format, chain GA [auth B] SDF format, chain GB [auth D] SDF format, chain GD [auth I] SDF format, chain HA [auth B] SDF format, chain HB [auth D] SDF format, chain HD [auth I] SDF format, chain IA [auth B] SDF format, chain IC [auth G] SDF format, chain ID [auth I] SDF format, chain JC [auth G] SDF format, chain JD [auth I] SDF format, chain KC [auth G] SDF format, chain KD [auth I] SDF format, chain LA [auth C] SDF format, chain LB [auth E] SDF format, chain LC [auth G] SDF format, chain LD [auth I] SDF format, chain MA [auth C] SDF format, chain MB [auth E] SDF format, chain MC [auth G] SDF format, chain N [auth A] SDF format, chain NA [auth C] SDF format, chain NB [auth E] SDF format, chain NC [auth G] SDF format, chain O [auth A] SDF format, chain OA [auth C] SDF format, chain OB [auth E] SDF format, chain OC [auth G] SDF format, chain OD [auth J] SDF format, chain P [auth A] SDF format, chain PA [auth C] SDF format, chain PB [auth E] SDF format, chain PC [auth G] SDF format, chain PD [auth J] SDF format, chain Q [auth A] SDF format, chain QA [auth C] SDF format, chain QB [auth E] SDF format, chain QD [auth J] SDF format, chain R [auth A] SDF format, chain RA [auth C] SDF format, chain RB [auth E] SDF format, chain RC [auth H] SDF format, chain RD [auth J] SDF format, chain S [auth A] SDF format, chain SA [auth C] SDF format, chain SC [auth H] SDF format, chain SD [auth J] SDF format, chain T [auth A] SDF format, chain TA [auth C] SDF format, chain TC [auth H] SDF format, chain TD [auth J] SDF format, chain U [auth A] SDF format, chain UA [auth C] SDF format, chain UC [auth H] SDF format, chain UD [auth J] SDF format, chain V [auth A] SDF format, chain VA [auth C] SDF format, chain VB [auth F] SDF format, chain VC [auth H] SDF format, chain WB [auth F] SDF format, chain WC [auth H] SDF format, chain XA [auth D] SDF format, chain XB [auth F] SDF format, chain XC [auth H] SDF format, chain YA [auth D] SDF format, chain YB [auth F] SDF format, chain YC [auth H] SDF format, chain ZA [auth D] SDF format, chain ZB [auth F] SDF format, chain ZC [auth H] MOL2 format, chain AB [auth D] MOL2 format, chain AC [auth F] MOL2 format, chain AD [auth H] MOL2 format, chain BA [auth B] MOL2 format, chain BB [auth D] MOL2 format, chain BC [auth F] MOL2 format, chain BD [auth H] MOL2 format, chain CA [auth B] MOL2 format, chain CB [auth D] MOL2 format, chain CC [auth F] MOL2 format, chain CD [auth H] MOL2 format, chain DA [auth B] MOL2 format, chain DB [auth D] MOL2 format, chain DC [auth F] MOL2 format, chain DD [auth I] MOL2 format, chain EA [auth B] MOL2 format, chain EB [auth D] MOL2 format, chain ED [auth I] MOL2 format, chain FA [auth B] MOL2 format, chain FB [auth D] MOL2 format, chain FD [auth I] MOL2 format, chain GA [auth B] MOL2 format, chain GB [auth D] MOL2 format, chain GD [auth I] MOL2 format, chain HA [auth B] MOL2 format, chain HB [auth D] MOL2 format, chain HD [auth I] MOL2 format, chain IA [auth B] MOL2 format, chain IC [auth G] MOL2 format, chain ID [auth I] MOL2 format, chain JC [auth G] MOL2 format, chain JD [auth I] MOL2 format, chain KC [auth G] MOL2 format, chain KD [auth I] MOL2 format, chain LA [auth C] MOL2 format, chain LB [auth E] MOL2 format, chain LC [auth G] MOL2 format, chain LD [auth I] MOL2 format, chain MA [auth C] MOL2 format, chain MB [auth E] MOL2 format, chain MC [auth G] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth C] MOL2 format, chain NB [auth E] MOL2 format, chain NC [auth G] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth C] MOL2 format, chain OB [auth E] MOL2 format, chain OC [auth G] MOL2 format, chain OD [auth J] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth C] MOL2 format, chain PB [auth E] MOL2 format, chain PC [auth G] MOL2 format, chain PD [auth J] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth C] MOL2 format, chain QB [auth E] MOL2 format, chain QD [auth J] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth C] MOL2 format, chain RB [auth E] MOL2 format, chain RC [auth H] MOL2 format, chain RD [auth J] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth C] MOL2 format, chain SC [auth H] MOL2 format, chain SD [auth J] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth C] MOL2 format, chain TC [auth H] MOL2 format, chain TD [auth J] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth C] MOL2 format, chain UC [auth H] MOL2 format, chain UD [auth J] MOL2 format, chain V [auth A] MOL2 format, chain VA [auth C] MOL2 format, chain VB [auth F] MOL2 format, chain VC [auth H] MOL2 format, chain WB [auth F] MOL2 format, chain WC [auth H] MOL2 format, chain XA [auth D] MOL2 format, chain XB [auth F] MOL2 format, chain XC [auth H] MOL2 format, chain YA [auth D] MOL2 format, chain YB [auth F] MOL2 format, chain YC [auth H] MOL2 format, chain ZA [auth D] MOL2 format, chain ZB [auth F] MOL2 format, chain ZC [auth H]	AB [auth D] AC [auth F] AD [auth H] BA [auth B] BB [auth D] AB [auth D], AC [auth F], AD [auth H], BA [auth B], BB [auth D], BC [auth F], BD [auth H], CA [auth B], CB [auth D], CC [auth F], CD [auth H], DA [auth B], DB [auth D], DC [auth F], DD [auth I], EA [auth B], EB [auth D], ED [auth I], FA [auth B], FB [auth D], FD [auth I], GA [auth B], GB [auth D], GD [auth I], HA [auth B], HB [auth D], HD [auth I], IA [auth B], IC [auth G], ID [auth I], JC [auth G], JD [auth I], KC [auth G], KD [auth I], LA [auth C], LB [auth E], LC [auth G], LD [auth I], MA [auth C], MB [auth E], MC [auth G], N [auth A], NA [auth C], NB [auth E], NC [auth G], O [auth A], OA [auth C], OB [auth E], OC [auth G], OD [auth J], P [auth A], PA [auth C], PB [auth E], PC [auth G], PD [auth J], Q [auth A], QA [auth C], QB [auth E], QD [auth J], R [auth A], RA [auth C], RB [auth E], RC [auth H], RD [auth J], S [auth A], SA [auth C], SC [auth H], SD [auth J], T [auth A], TA [auth C], TC [auth H], TD [auth J], U [auth A], UA [auth C], UC [auth H], UD [auth J], V [auth A], VA [auth C], VB [auth F], VC [auth H], WB [auth F], WC [auth H], XA [auth D], XB [auth F], XC [auth H], YA [auth D], YB [auth F], YC [auth H], ZA [auth D], ZB [auth F], ZC [auth H]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AB [auth D] Focus chain AC [auth F] Focus chain AD [auth H] Focus chain BA [auth B] Focus chain BB [auth D] Focus chain BC [auth F] Focus chain BD [auth H] Focus chain CA [auth B] Focus chain CB [auth D] Focus chain CC [auth F] Focus chain CD [auth H] Focus chain DA [auth B] Focus chain DB [auth D] Focus chain DC [auth F] Focus chain DD [auth I] Focus chain EA [auth B] Focus chain EB [auth D] Focus chain ED [auth I] Focus chain FA [auth B] Focus chain FB [auth D] Focus chain FD [auth I] Focus chain GA [auth B] Focus chain GB [auth D] Focus chain GD [auth I] Focus chain HA [auth B] Focus chain HB [auth D] Focus chain HD [auth I] Focus chain IA [auth B] Focus chain IC [auth G] Focus chain ID [auth I] Focus chain JC [auth G] Focus chain JD [auth I] Focus chain KC [auth G] Focus chain KD [auth I] Focus chain LA [auth C] Focus chain LB [auth E] Focus chain LC [auth G] Focus chain LD [auth I] Focus chain MA [auth C] Focus chain MB [auth E] Focus chain MC [auth G] Focus chain N [auth A] Focus chain NA [auth C] Focus chain NB [auth E] Focus chain NC [auth G] Focus chain O [auth A] Focus chain OA [auth C] Focus chain OB [auth E] Focus chain OC [auth G] Focus chain OD [auth J] Focus chain P [auth A] Focus chain PA [auth C] Focus chain PB [auth E] Focus chain PC [auth G] Focus chain PD [auth J] Focus chain Q [auth A] Focus chain QA [auth C] Focus chain QB [auth E] Focus chain QD [auth J] Focus chain R [auth A] Focus chain RA [auth C] Focus chain RB [auth E] Focus chain RC [auth H] Focus chain RD [auth J] Focus chain S [auth A] Focus chain SA [auth C] Focus chain SC [auth H] Focus chain SD [auth J] Focus chain T [auth A] Focus chain TA [auth C] Focus chain TC [auth H] Focus chain TD [auth J] Focus chain U [auth A] Focus chain UA [auth C] Focus chain UC [auth H] Focus chain UD [auth J] Focus chain V [auth A] Focus chain VA [auth C] Focus chain VB [auth F] Focus chain VC [auth H] Focus chain WB [auth F] Focus chain WC [auth H] Focus chain XA [auth D] Focus chain XB [auth F] Focus chain XC [auth H] Focus chain YA [auth D] Focus chain YB [auth F] Focus chain YC [auth H] Focus chain ZA [auth D] Focus chain ZB [auth F] Focus chain ZC [auth H] Interactions & Density Focus chain AB [auth D] Focus chain AC [auth F] Focus chain AD [auth H] Focus chain BA [auth B] Focus chain BB [auth D] Focus chain BC [auth F] Focus chain BD [auth H] Focus chain CA [auth B] Focus chain CB [auth D] Focus chain CC [auth F] Focus chain CD [auth H] Focus chain DA [auth B] Focus chain DB [auth D] Focus chain DC [auth F] Focus chain DD [auth I] Focus chain EA [auth B] Focus chain EB [auth D] Focus chain ED [auth I] Focus chain FA [auth B] Focus chain FB [auth D] Focus chain FD [auth I] Focus chain GA [auth B] Focus chain GB [auth D] Focus chain GD [auth I] Focus chain HA [auth B] Focus chain HB [auth D] Focus chain HD [auth I] Focus chain IA [auth B] Focus chain IC [auth G] Focus chain ID [auth I] Focus chain JC [auth G] Focus chain JD [auth I] Focus chain KC [auth G] Focus chain KD [auth I] Focus chain LA [auth C] Focus chain LB [auth E] Focus chain LC [auth G] Focus chain LD [auth I] Focus chain MA [auth C] Focus chain MB [auth E] Focus chain MC [auth G] Focus chain N [auth A] Focus chain NA [auth C] Focus chain NB [auth E] Focus chain NC [auth G] Focus chain O [auth A] Focus chain OA [auth C] Focus chain OB [auth E] Focus chain OC [auth G] Focus chain OD [auth J] Focus chain P [auth A] Focus chain PA [auth C] Focus chain PB [auth E] Focus chain PC [auth G] Focus chain PD [auth J] Focus chain Q [auth A] Focus chain QA [auth C] Focus chain QB [auth E] Focus chain QD [auth J] Focus chain R [auth A] Focus chain RA [auth C] Focus chain RB [auth E] Focus chain RC [auth H] Focus chain RD [auth J] Focus chain S [auth A] Focus chain SA [auth C] Focus chain SC [auth H] Focus chain SD [auth J] Focus chain T [auth A] Focus chain TA [auth C] Focus chain TC [auth H] Focus chain TD [auth J] Focus chain U [auth A] Focus chain UA [auth C] Focus chain UC [auth H] Focus chain UD [auth J] Focus chain V [auth A] Focus chain VA [auth C] Focus chain VB [auth F] Focus chain VC [auth H] Focus chain WB [auth F] Focus chain WC [auth H] Focus chain XA [auth D] Focus chain XB [auth F] Focus chain XC [auth H] Focus chain YA [auth D] Focus chain YB [auth F] Focus chain YC [auth H] Focus chain ZA [auth D] Focus chain ZB [auth F] Focus chain ZC [auth H]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain EC [auth F] SDF format, chain FC [auth F] SDF format, chain GC [auth F] SDF format, chain HC [auth F] SDF format, chain IB [auth D] SDF format, chain JA [auth B] SDF format, chain KA [auth B] SDF format, chain MD [auth I] SDF format, chain ND [auth I] SDF format, chain QC [auth G] SDF format, chain SB [auth E] SDF format, chain TB [auth E] SDF format, chain UB [auth E] SDF format, chain VD [auth J] SDF format, chain W [auth A] SDF format, chain WA [auth C] SDF format, chain WD [auth J] SDF format, chain X [auth A] SDF format, chain XD [auth J] SDF format, chain Y [auth A] SDF format, chain YD [auth J] SDF format, chain Z [auth A] SDF format, chain ZD [auth J] MOL2 format, chain EC [auth F] MOL2 format, chain FC [auth F] MOL2 format, chain GC [auth F] MOL2 format, chain HC [auth F] MOL2 format, chain IB [auth D] MOL2 format, chain JA [auth B] MOL2 format, chain KA [auth B] MOL2 format, chain MD [auth I] MOL2 format, chain ND [auth I] MOL2 format, chain QC [auth G] MOL2 format, chain SB [auth E] MOL2 format, chain TB [auth E] MOL2 format, chain UB [auth E] MOL2 format, chain VD [auth J] MOL2 format, chain W [auth A] MOL2 format, chain WA [auth C] MOL2 format, chain WD [auth J] MOL2 format, chain X [auth A] MOL2 format, chain XD [auth J] MOL2 format, chain Y [auth A] MOL2 format, chain YD [auth J] MOL2 format, chain Z [auth A] MOL2 format, chain ZD [auth J]	EC [auth F] FC [auth F] GC [auth F] HC [auth F] IB [auth D] EC [auth F], FC [auth F], GC [auth F], HC [auth F], IB [auth D], JA [auth B], KA [auth B], MD [auth I], ND [auth I], QC [auth G], SB [auth E], TB [auth E], UB [auth E], VD [auth J], W [auth A], WA [auth C], WD [auth J], X [auth A], XD [auth J], Y [auth A], YD [auth J], Z [auth A], ZD [auth J]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain EC [auth F] Focus chain FC [auth F] Focus chain GC [auth F] Focus chain HC [auth F] Focus chain IB [auth D] Focus chain JA [auth B] Focus chain KA [auth B] Focus chain MD [auth I] Focus chain ND [auth I] Focus chain QC [auth G] Focus chain SB [auth E] Focus chain TB [auth E] Focus chain UB [auth E] Focus chain VD [auth J] Focus chain W [auth A] Focus chain WA [auth C] Focus chain WD [auth J] Focus chain X [auth A] Focus chain XD [auth J] Focus chain Y [auth A] Focus chain YD [auth J] Focus chain Z [auth A] Focus chain ZD [auth J] Interactions & Density Focus chain EC [auth F] Focus chain FC [auth F] Focus chain GC [auth F] Focus chain HC [auth F] Focus chain IB [auth D] Focus chain JA [auth B] Focus chain KA [auth B] Focus chain MD [auth I] Focus chain ND [auth I] Focus chain QC [auth G] Focus chain SB [auth E] Focus chain TB [auth E] Focus chain UB [auth E] Focus chain VD [auth J] Focus chain W [auth A] Focus chain WA [auth C] Focus chain WD [auth J] Focus chain X [auth A] Focus chain XD [auth J] Focus chain Y [auth A] Focus chain YD [auth J] Focus chain Z [auth A] Focus chain ZD [auth J]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900003 Query on PRD_900003	K	sucrose	Oligosaccharide / Nutrient		Interactions Focus chain K Interactions & Density Focus chain K

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.219
R-Value Work: 0.189
R-Value Observed: 0.190
Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 203.349	α = 90
b = 203.349	β = 90
c = 157.775	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2020-05-06

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2020-05-06
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2023-06-14
Changes: Database references, Structure summary
Version 2.2: 2023-10-25
Changes: Data collection, Refinement description