1UR9

Interactions of a family 18 chitinase with the designed inhibitor HM508, and its degradation product, chitobiono-delta-lactone

PDB DOI: https://doi.org/10.2210/pdb1UR9/pdb

Classification: HYDROLASE
Organism(s): Serratia marcescens
Expression System: Escherichia coli DH5[alpha]
Mutation(s): Yes

Deposited: 2003-10-27 Released: 2004-04-27
Deposition Author(s): Vaaje-Kolstad, G., Vasella, A., Peter, M.G., Netter, C., Houston, D.R., Westereng, B., Synstad, B., Eijsink, V.G.H., Van Aalten, D.M.F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.255
R-Value Work: 0.208
R-Value Observed: 0.208

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 119.11 kDa
Atom Count: 9,198
Modelled Residue Count: 995
Deposited Residue Count: 998
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CHITINASE B	A, B	499	Serratia marcescens	Mutation(s): 1 EC: 3.2.1.14
UniProt
Find proteins for Q54276 (Serratia marcescens) Explore Q54276 Go to UniProtKB: Q54276
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q54276
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-(acetylamido)-2-deoxy-D-glucono-1,5-lactone	C, D	2		N/A	Interactions Focus chain C Focus chain D Interactions & Density Focus chain C Focus chain D
Glycosylation Resources
GlyTouCan: G08176ED GlyCosmos: G08176ED

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PHJ Query on PHJ Download Ideal Coordinates CCD File SDF format, chain AC [auth B] SDF format, chain PA [auth A] MOL2 format, chain AC [auth B] MOL2 format, chain PA [auth A]	AC [auth B], PA [auth A]	N-[(AMINOOXY)CARBONYL]-N-PHENYLAMINE C₇ H₈ N₂ O₂ YQHOHPOCZUAUKP-UHFFFAOYSA-N		Interactions Focus chain AC [auth B] Focus chain PA [auth A] Interactions & Density Focus chain AC [auth B] Focus chain PA [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain IA [auth A] SDF format, chain JA [auth A] SDF format, chain KA [auth A] SDF format, chain LA [auth A] SDF format, chain MA [auth A] SDF format, chain NA [auth A] SDF format, chain WB [auth B] SDF format, chain XB [auth B] SDF format, chain YB [auth B] MOL2 format, chain IA [auth A] MOL2 format, chain JA [auth A] MOL2 format, chain KA [auth A] MOL2 format, chain LA [auth A] MOL2 format, chain MA [auth A] MOL2 format, chain NA [auth A] MOL2 format, chain WB [auth B] MOL2 format, chain XB [auth B] MOL2 format, chain YB [auth B]	IA [auth A] JA [auth A] KA [auth A] LA [auth A] MA [auth A] IA [auth A], JA [auth A], KA [auth A], LA [auth A], MA [auth A], NA [auth A], WB [auth B], XB [auth B], YB [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain IA [auth A] Focus chain JA [auth A] Focus chain KA [auth A] Focus chain LA [auth A] Focus chain MA [auth A] Focus chain NA [auth A] Focus chain WB [auth B] Focus chain XB [auth B] Focus chain YB [auth B] Interactions & Density Focus chain IA [auth A] Focus chain JA [auth A] Focus chain KA [auth A] Focus chain LA [auth A] Focus chain MA [auth A] Focus chain NA [auth A] Focus chain WB [auth B] Focus chain XB [auth B] Focus chain YB [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain AB [auth B] SDF format, chain BA [auth A] SDF format, chain BB [auth B] SDF format, chain CA [auth A] SDF format, chain CB [auth B] SDF format, chain DA [auth A] SDF format, chain DB [auth B] SDF format, chain E [auth A] SDF format, chain EA [auth A] SDF format, chain EB [auth B] SDF format, chain F [auth A] SDF format, chain FA [auth A] SDF format, chain FB [auth B] SDF format, chain G [auth A] SDF format, chain GA [auth A] SDF format, chain GB [auth B] SDF format, chain H [auth A] SDF format, chain HA [auth A] SDF format, chain HB [auth B] SDF format, chain I [auth A] SDF format, chain IB [auth B] SDF format, chain J [auth A] SDF format, chain JB [auth B] SDF format, chain K [auth A] SDF format, chain KB [auth B] SDF format, chain L [auth A] SDF format, chain LB [auth B] SDF format, chain M [auth A] SDF format, chain MB [auth B] SDF format, chain N [auth A] SDF format, chain NB [auth B] SDF format, chain O [auth A] SDF format, chain OA [auth A] SDF format, chain OB [auth B] SDF format, chain P [auth A] SDF format, chain PB [auth B] SDF format, chain Q [auth A] SDF format, chain QA [auth B] SDF format, chain QB [auth B] SDF format, chain R [auth A] SDF format, chain RA [auth B] SDF format, chain RB [auth B] SDF format, chain S [auth A] SDF format, chain SA [auth B] SDF format, chain SB [auth B] SDF format, chain T [auth A] SDF format, chain TA [auth B] SDF format, chain TB [auth B] SDF format, chain U [auth A] SDF format, chain UA [auth B] SDF format, chain UB [auth B] SDF format, chain V [auth A] SDF format, chain VA [auth B] SDF format, chain VB [auth B] SDF format, chain W [auth A] SDF format, chain WA [auth B] SDF format, chain X [auth A] SDF format, chain XA [auth B] SDF format, chain Y [auth A] SDF format, chain YA [auth B] SDF format, chain Z [auth A] SDF format, chain ZA [auth B] SDF format, chain ZB [auth B] MOL2 format, chain AA [auth A] MOL2 format, chain AB [auth B] MOL2 format, chain BA [auth A] MOL2 format, chain BB [auth B] MOL2 format, chain CA [auth A] MOL2 format, chain CB [auth B] MOL2 format, chain DA [auth A] MOL2 format, chain DB [auth B] MOL2 format, chain E [auth A] MOL2 format, chain EA [auth A] MOL2 format, chain EB [auth B] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth A] MOL2 format, chain FB [auth B] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth A] MOL2 format, chain GB [auth B] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth A] MOL2 format, chain HB [auth B] MOL2 format, chain I [auth A] MOL2 format, chain IB [auth B] MOL2 format, chain J [auth A] MOL2 format, chain JB [auth B] MOL2 format, chain K [auth A] MOL2 format, chain KB [auth B] MOL2 format, chain L [auth A] MOL2 format, chain LB [auth B] MOL2 format, chain M [auth A] MOL2 format, chain MB [auth B] MOL2 format, chain N [auth A] MOL2 format, chain NB [auth B] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth A] MOL2 format, chain OB [auth B] MOL2 format, chain P [auth A] MOL2 format, chain PB [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth B] MOL2 format, chain QB [auth B] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth B] MOL2 format, chain RB [auth B] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth B] MOL2 format, chain SB [auth B] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth B] MOL2 format, chain TB [auth B] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth B] MOL2 format, chain UB [auth B] MOL2 format, chain V [auth A] MOL2 format, chain VA [auth B] MOL2 format, chain VB [auth B] MOL2 format, chain W [auth A] MOL2 format, chain WA [auth B] MOL2 format, chain X [auth A] MOL2 format, chain XA [auth B] MOL2 format, chain Y [auth A] MOL2 format, chain YA [auth B] MOL2 format, chain Z [auth A] MOL2 format, chain ZA [auth B] MOL2 format, chain ZB [auth B]	AA [auth A] AB [auth B] BA [auth A] BB [auth B] CA [auth A] AA [auth A], AB [auth B], BA [auth A], BB [auth B], CA [auth A], CB [auth B], DA [auth A], DB [auth B], E [auth A], EA [auth A], EB [auth B], F [auth A], FA [auth A], FB [auth B], G [auth A], GA [auth A], GB [auth B], H [auth A], HA [auth A], HB [auth B], I [auth A], IB [auth B], J [auth A], JB [auth B], K [auth A], KB [auth B], L [auth A], LB [auth B], M [auth A], MB [auth B], N [auth A], NB [auth B], O [auth A], OA [auth A], OB [auth B], P [auth A], PB [auth B], Q [auth A], QA [auth B], QB [auth B], R [auth A], RA [auth B], RB [auth B], S [auth A], SA [auth B], SB [auth B], T [auth A], TA [auth B], TB [auth B], U [auth A], UA [auth B], UB [auth B], V [auth A], VA [auth B], VB [auth B], W [auth A], WA [auth B], X [auth A], XA [auth B], Y [auth A], YA [auth B], Z [auth A], ZA [auth B], ZB [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain AB [auth B] Focus chain BA [auth A] Focus chain BB [auth B] Focus chain CA [auth A] Focus chain CB [auth B] Focus chain DA [auth A] Focus chain DB [auth B] Focus chain E [auth A] Focus chain EA [auth A] Focus chain EB [auth B] Focus chain F [auth A] Focus chain FA [auth A] Focus chain FB [auth B] Focus chain G [auth A] Focus chain GA [auth A] Focus chain GB [auth B] Focus chain H [auth A] Focus chain HA [auth A] Focus chain HB [auth B] Focus chain I [auth A] Focus chain IB [auth B] Focus chain J [auth A] Focus chain JB [auth B] Focus chain K [auth A] Focus chain KB [auth B] Focus chain L [auth A] Focus chain LB [auth B] Focus chain M [auth A] Focus chain MB [auth B] Focus chain N [auth A] Focus chain NB [auth B] Focus chain O [auth A] Focus chain OA [auth A] Focus chain OB [auth B] Focus chain P [auth A] Focus chain PB [auth B] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain QB [auth B] Focus chain R [auth A] Focus chain RA [auth B] Focus chain RB [auth B] Focus chain S [auth A] Focus chain SA [auth B] Focus chain SB [auth B] Focus chain T [auth A] Focus chain TA [auth B] Focus chain TB [auth B] Focus chain U [auth A] Focus chain UA [auth B] Focus chain UB [auth B] Focus chain V [auth A] Focus chain VA [auth B] Focus chain VB [auth B] Focus chain W [auth A] Focus chain WA [auth B] Focus chain X [auth A] Focus chain XA [auth B] Focus chain Y [auth A] Focus chain YA [auth B] Focus chain Z [auth A] Focus chain ZA [auth B] Focus chain ZB [auth B] Interactions & Density Focus chain AA [auth A] Focus chain AB [auth B] Focus chain BA [auth A] Focus chain BB [auth B] Focus chain CA [auth A] Focus chain CB [auth B] Focus chain DA [auth A] Focus chain DB [auth B] Focus chain E [auth A] Focus chain EA [auth A] Focus chain EB [auth B] Focus chain F [auth A] Focus chain FA [auth A] Focus chain FB [auth B] Focus chain G [auth A] Focus chain GA [auth A] Focus chain GB [auth B] Focus chain H [auth A] Focus chain HA [auth A] Focus chain HB [auth B] Focus chain I [auth A] Focus chain IB [auth B] Focus chain J [auth A] Focus chain JB [auth B] Focus chain K [auth A] Focus chain KB [auth B] Focus chain L [auth A] Focus chain LB [auth B] Focus chain M [auth A] Focus chain MB [auth B] Focus chain N [auth A] Focus chain NB [auth B] Focus chain O [auth A] Focus chain OA [auth A] Focus chain OB [auth B] Focus chain P [auth A] Focus chain PB [auth B] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain QB [auth B] Focus chain R [auth A] Focus chain RA [auth B] Focus chain RB [auth B] Focus chain S [auth A] Focus chain SA [auth B] Focus chain SB [auth B] Focus chain T [auth A] Focus chain TA [auth B] Focus chain TB [auth B] Focus chain U [auth A] Focus chain UA [auth B] Focus chain UB [auth B] Focus chain V [auth A] Focus chain VA [auth B] Focus chain VB [auth B] Focus chain W [auth A] Focus chain WA [auth B] Focus chain X [auth A] Focus chain XA [auth B] Focus chain Y [auth A] Focus chain YA [auth B] Focus chain Z [auth A] Focus chain ZA [auth B] Focus chain ZB [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.255
R-Value Work: 0.208
R-Value Observed: 0.208
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.524	α = 90
b = 104.177	β = 90
c = 185.992	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2004-04-27

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2004-04-27
Type: Initial release
Version 1.1: 2015-04-15
Changes: Database references, Derived calculations, Non-polymer description, Other, Refinement description, Source and taxonomy, Structure summary, Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary
Version 2.1: 2023-12-13
Changes: Data collection, Database references, Refinement description, Structure summary