2VXJ

CRYSTAL STRUCTURE OF PA-IL LECTIN COMPLEXED WITH AGAL13BGAL14GLC AT 1.9 A RESOLUTION

PDB DOI: https://doi.org/10.2210/pdb2VXJ/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Pseudomonas aeruginosa PAO1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2008-07-04 Released: 2008-09-16
Deposition Author(s): Blanchard, B., Nurisso, A., Hollville, E., Tetaud, C., Wiels, J., Pokorna, M., Wimmerova, M., Varrot, A., Imberty, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.245
R-Value Work: 0.185
R-Value Observed: 0.188

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: 320.81 kDa
Atom Count: 25,600
Modelled Residue Count: 2,896
Deposited Residue Count: 2,904
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PA-I GALACTOPHILIC LECTIN	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X	121	Pseudomonas aeruginosa PAO1	Mutation(s): 0
UniProt
Find proteins for Q05097 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q05097 Go to UniProtKB: Q05097
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q05097
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-galactopyranose-(1-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose	BA [auth b], DA [auth d], EA [auth e], FA [auth f], GA [auth g], BA [auth b], DA [auth d], EA [auth e], FA [auth f], GA [auth g], HA [auth h], IA [auth i], JA [auth j], KA [auth k], MA [auth m], NA [auth n], OA [auth o], PA [auth p], QA [auth q], RA [auth r], SA [auth s], TA [auth t], UA [auth u], VA [auth v], Y, Z	3		N/A	Interactions Focus chain BA [auth b] Focus chain DA [auth d] Focus chain EA [auth e] Focus chain FA [auth f] Focus chain GA [auth g] Focus chain HA [auth h] Focus chain IA [auth i] Focus chain JA [auth j] Focus chain KA [auth k] Focus chain MA [auth m] Focus chain NA [auth n] Focus chain OA [auth o] Focus chain PA [auth p] Focus chain QA [auth q] Focus chain RA [auth r] Focus chain SA [auth s] Focus chain TA [auth t] Focus chain UA [auth u] Focus chain VA [auth v] Focus chain Y Focus chain Z Interactions & Density Focus chain BA [auth b] Focus chain DA [auth d] Focus chain EA [auth e] Focus chain FA [auth f] Focus chain GA [auth g] Focus chain HA [auth h] Focus chain IA [auth i] Focus chain JA [auth j] Focus chain KA [auth k] Focus chain MA [auth m] Focus chain NA [auth n] Focus chain OA [auth o] Focus chain PA [auth p] Focus chain QA [auth q] Focus chain RA [auth r] Focus chain SA [auth s] Focus chain TA [auth t] Focus chain UA [auth u] Focus chain VA [auth v] Focus chain Y Focus chain Z
Glycosylation Resources
GlyTouCan: G78074HX GlyCosmos: G78074HX GlyGen: G78074HX

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-galactopyranose-(1-3)-beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose	AA [auth a], CA [auth c]	3		N/A	Interactions Focus chain AA [auth a] Focus chain CA [auth c] Interactions & Density Focus chain AA [auth a] Focus chain CA [auth c]
Glycosylation Resources
GlyTouCan: G57666OY GlyCosmos: G57666OY GlyGen: G57666OY

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-galactopyranose-(1-3)-beta-D-galactopyranose	LA [auth l]	2		N/A	Interactions Focus chain LA [auth l] Interactions & Density Focus chain LA [auth l]
Glycosylation Resources
GlyTouCan: G24432YB GlyCosmos: G24432YB GlyGen: G24432YB

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BGC Query on BGC Download Ideal Coordinates CCD File SDF format, chain UB [auth N] MOL2 format, chain UB [auth N]	UB [auth N]	beta-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-VFUOTHLCSA-N		Interactions Focus chain UB [auth N] Interactions & Density Focus chain UB [auth N]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain IB [auth H] SDF format, chain AC [auth Q] SDF format, chain BB [auth D] SDF format, chain BC [auth Q] SDF format, chain DB [auth E] SDF format, chain EC [auth S] SDF format, chain GB [auth G] SDF format, chain HC [auth U] SDF format, chain JC [auth V] SDF format, chain KB [auth I] SDF format, chain LB [auth I] SDF format, chain LC [auth W] SDF format, chain MC [auth W] SDF format, chain OC [auth X] SDF format, chain PB [auth L] SDF format, chain RB [auth M] SDF format, chain SB [auth M] SDF format, chain VB [auth N] SDF format, chain XA [auth A] SDF format, chain XB [auth O] MOL2 format, chain IB [auth H] MOL2 format, chain AC [auth Q] MOL2 format, chain BB [auth D] MOL2 format, chain BC [auth Q] MOL2 format, chain DB [auth E] MOL2 format, chain EC [auth S] MOL2 format, chain GB [auth G] MOL2 format, chain HC [auth U] MOL2 format, chain JC [auth V] MOL2 format, chain KB [auth I] MOL2 format, chain LB [auth I] MOL2 format, chain LC [auth W] MOL2 format, chain MC [auth W] MOL2 format, chain OC [auth X] MOL2 format, chain PB [auth L] MOL2 format, chain RB [auth M] MOL2 format, chain SB [auth M] MOL2 format, chain VB [auth N] MOL2 format, chain XA [auth A] MOL2 format, chain XB [auth O]	AC [auth Q] BB [auth D] BC [auth Q] DB [auth E] EC [auth S] AC [auth Q], BB [auth D], BC [auth Q], DB [auth E], EC [auth S], GB [auth G], HC [auth U], IB [auth H], JC [auth V], KB [auth I], LB [auth I], LC [auth W], MC [auth W], OC [auth X], PB [auth L], RB [auth M], SB [auth M], VB [auth N], XA [auth A], XB [auth O]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AC [auth Q] Focus chain BB [auth D] Focus chain BC [auth Q] Focus chain DB [auth E] Focus chain EC [auth S] Focus chain GB [auth G] Focus chain HC [auth U] Focus chain IB [auth H] Focus chain JC [auth V] Focus chain KB [auth I] Focus chain LB [auth I] Focus chain LC [auth W] Focus chain MC [auth W] Focus chain OC [auth X] Focus chain PB [auth L] Focus chain RB [auth M] Focus chain SB [auth M] Focus chain VB [auth N] Focus chain XA [auth A] Focus chain XB [auth O] Interactions & Density Focus chain AC [auth Q] Focus chain BB [auth D] Focus chain BC [auth Q] Focus chain DB [auth E] Focus chain EC [auth S] Focus chain GB [auth G] Focus chain HC [auth U] Focus chain IB [auth H] Focus chain JC [auth V] Focus chain KB [auth I] Focus chain LB [auth I] Focus chain LC [auth W] Focus chain MC [auth W] Focus chain OC [auth X] Focus chain PB [auth L] Focus chain RB [auth M] Focus chain SB [auth M] Focus chain VB [auth N] Focus chain XA [auth A] Focus chain XB [auth O]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain CB [auth E] SDF format, chain FB [auth G] SDF format, chain FC [auth T] SDF format, chain JB [auth I] SDF format, chain NB [auth K] SDF format, chain NC [auth X] SDF format, chain QB [auth M] SDF format, chain YA [auth B] SDF format, chain AB [auth D] SDF format, chain CC [auth R] SDF format, chain DC [auth S] SDF format, chain EB [auth F] SDF format, chain GC [auth U] SDF format, chain HB [auth H] SDF format, chain IC [auth V] SDF format, chain KC [auth W] SDF format, chain MB [auth J] SDF format, chain OB [auth L] SDF format, chain TB [auth N] SDF format, chain WA [auth A] SDF format, chain WB [auth O] SDF format, chain YB [auth P] SDF format, chain ZA [auth C] SDF format, chain ZB [auth Q] MOL2 format, chain CB [auth E] MOL2 format, chain FB [auth G] MOL2 format, chain FC [auth T] MOL2 format, chain JB [auth I] MOL2 format, chain NB [auth K] MOL2 format, chain NC [auth X] MOL2 format, chain QB [auth M] MOL2 format, chain YA [auth B] MOL2 format, chain AB [auth D] MOL2 format, chain CC [auth R] MOL2 format, chain DC [auth S] MOL2 format, chain EB [auth F] MOL2 format, chain GC [auth U] MOL2 format, chain HB [auth H] MOL2 format, chain IC [auth V] MOL2 format, chain KC [auth W] MOL2 format, chain MB [auth J] MOL2 format, chain OB [auth L] MOL2 format, chain TB [auth N] MOL2 format, chain WA [auth A] MOL2 format, chain WB [auth O] MOL2 format, chain YB [auth P] MOL2 format, chain ZA [auth C] MOL2 format, chain ZB [auth Q]	AB [auth D] CB [auth E] CC [auth R] DC [auth S] EB [auth F] AB [auth D], CB [auth E], CC [auth R], DC [auth S], EB [auth F], FB [auth G], FC [auth T], GC [auth U], HB [auth H], IC [auth V], JB [auth I], KC [auth W], MB [auth J], NB [auth K], NC [auth X], OB [auth L], QB [auth M], TB [auth N], WA [auth A], WB [auth O], YA [auth B], YB [auth P], ZA [auth C], ZB [auth Q]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AB [auth D] Focus chain CB [auth E] Focus chain CC [auth R] Focus chain DC [auth S] Focus chain EB [auth F] Focus chain FB [auth G] Focus chain FC [auth T] Focus chain GC [auth U] Focus chain HB [auth H] Focus chain IC [auth V] Focus chain JB [auth I] Focus chain KC [auth W] Focus chain MB [auth J] Focus chain NB [auth K] Focus chain NC [auth X] Focus chain OB [auth L] Focus chain QB [auth M] Focus chain TB [auth N] Focus chain WA [auth A] Focus chain WB [auth O] Focus chain YA [auth B] Focus chain YB [auth P] Focus chain ZA [auth C] Focus chain ZB [auth Q] Interactions & Density Focus chain AB [auth D] Focus chain CB [auth E] Focus chain CC [auth R] Focus chain DC [auth S] Focus chain EB [auth F] Focus chain FB [auth G] Focus chain FC [auth T] Focus chain GC [auth U] Focus chain HB [auth H] Focus chain IC [auth V] Focus chain JB [auth I] Focus chain KC [auth W] Focus chain MB [auth J] Focus chain NB [auth K] Focus chain NC [auth X] Focus chain OB [auth L] Focus chain QB [auth M] Focus chain TB [auth N] Focus chain WA [auth A] Focus chain WB [auth O] Focus chain YA [auth B] Focus chain YB [auth P] Focus chain ZA [auth C] Focus chain ZB [auth Q]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.245
R-Value Work: 0.185
R-Value Observed: 0.188
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.184	α = 93.93
b = 86.521	β = 98.16
c = 119.078	γ = 90.08

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-09-16

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-09-16
Type: Initial release
Version 1.1: 2011-08-03
Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary
Version 2.1: 2023-12-13
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary