2VNV

Crystal structure of BclA lectin from burkholderia cenocepacia in complex with alpha-methyl-mannoside at 1.7 Angstrom resolution

PDB DOI: https://doi.org/10.2210/pdb2VNV/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Burkholderia cenocepacia J2315
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2008-02-07 Released: 2008-04-08
Deposition Author(s): Lameignere, E., Malinovska, L., Mitchell, E.P., Imberty, A., Wimmerova, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.203
R-Value Work: 0.169
R-Value Observed: 0.171

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 71.31 kDa
Atom Count: 6,374
Modelled Residue Count: 631
Deposited Residue Count: 645
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BCLA	A, B, C, D, E	129	Burkholderia cenocepacia J2315	Mutation(s): 0
UniProt
Find proteins for B4EH87 (Burkholderia cenocepacia (strain ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610)) Explore B4EH87 Go to UniProtKB: B4EH87
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B4EH87
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MMA Query on MMA Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] SDF format, chain N [auth C] SDF format, chain Q [auth D] SDF format, chain U [auth E] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain N [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain U [auth E]	F [auth A], J [auth B], N [auth C], Q [auth D], U [auth E]	methyl alpha-D-mannopyranoside C₇ H₁₄ O₆ HOVAGTYPODGVJG-VEIUFWFVSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain Q [auth D] Focus chain U [auth E] Interactions & Density Focus chain F [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain Q [auth D] Focus chain U [auth E]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain M [auth B] SDF format, chain T [auth D] SDF format, chain X [auth E] MOL2 format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain T [auth D] MOL2 format, chain X [auth E]	I [auth A], M [auth B], T [auth D], X [auth E]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain I [auth A] Focus chain M [auth B] Focus chain T [auth D] Focus chain X [auth E] Interactions & Density Focus chain I [auth A] Focus chain M [auth B] Focus chain T [auth D] Focus chain X [auth E]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain R [auth D] SDF format, chain S [auth D] SDF format, chain V [auth E] SDF format, chain W [auth E] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain R [auth D] MOL2 format, chain S [auth D] MOL2 format, chain V [auth E] MOL2 format, chain W [auth E]	G [auth A] H [auth A] K [auth B] L [auth B] O [auth C] G [auth A], H [auth A], K [auth B], L [auth B], O [auth C], P [auth C], R [auth D], S [auth D], V [auth E], W [auth E]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain R [auth D] Focus chain S [auth D] Focus chain V [auth E] Focus chain W [auth E] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain R [auth D] Focus chain S [auth D] Focus chain V [auth E] Focus chain W [auth E]

Binding Affinity Annotations
ID	Source	Binding Affinity
MMA	Binding MOAD: 2VNV	Kd: 2750 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.203
R-Value Work: 0.169
R-Value Observed: 0.171
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.01	α = 90
b = 185.702	β = 90
c = 187.551	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-04-08

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-04-08
Type: Initial release
Version 1.1: 2011-05-10
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Other, Structure summary