4OWK

Crystal Structure of the Vibrio vulnificus Hemolysin/Cytolysin Beta-Trefoil Lectin with N-Acetyl-D-Galactosamine Bound

PDB DOI: https://doi.org/10.2210/pdb4OWK/pdb

Classification: TOXIN
Organism(s): Vibrio vulnificus CMCP6
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2014-02-02 Released: 2014-05-28
Deposition Author(s): Kaus, K., Olson, R.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.191
R-Value Work: 0.158
R-Value Observed: 0.159

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.8 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 110.04 kDa
Atom Count: 8,067
Modelled Residue Count: 924
Deposited Residue Count: 966
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytolysin	A, B, C, D, E A, B, C, D, E, F, G	138	Vibrio vulnificus CMCP6	Mutation(s): 0 Gene Names: VV2_0404, vvhA
UniProt
Find proteins for P19247 (Vibrio vulnificus (strain CMCP6)) Explore P19247 Go to UniProtKB: P19247
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P19247
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NGA Query on NGA Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain J [auth B] SDF format, chain K [auth C] SDF format, chain M [auth D] SDF format, chain O [auth E] SDF format, chain Q [auth F] SDF format, chain S [auth G] MOL2 format, chain H [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth C] MOL2 format, chain M [auth D] MOL2 format, chain O [auth E] MOL2 format, chain Q [auth F] MOL2 format, chain S [auth G]	H [auth A] J [auth B] K [auth C] M [auth D] O [auth E] H [auth A], J [auth B], K [auth C], M [auth D], O [auth E], Q [auth F], S [auth G]	2-acetamido-2-deoxy-beta-D-galactopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-JAJWTYFOSA-N		Interactions Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain O [auth E] Focus chain Q [auth F] Focus chain S [auth G] Interactions & Density Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain O [auth E] Focus chain Q [auth F] Focus chain S [auth G]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain P [auth E] SDF format, chain R [auth F] SDF format, chain I [auth A] SDF format, chain L [auth C] SDF format, chain N [auth D] SDF format, chain T [auth G] MOL2 format, chain P [auth E] MOL2 format, chain R [auth F] MOL2 format, chain I [auth A] MOL2 format, chain L [auth C] MOL2 format, chain N [auth D] MOL2 format, chain T [auth G]	I [auth A] L [auth C] N [auth D] P [auth E] R [auth F] I [auth A], L [auth C], N [auth D], P [auth E], R [auth F], T [auth G]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain L [auth C] Focus chain N [auth D] Focus chain P [auth E] Focus chain R [auth F] Focus chain T [auth G] Interactions & Density Focus chain I [auth A] Focus chain L [auth C] Focus chain N [auth D] Focus chain P [auth E] Focus chain R [auth F] Focus chain T [auth G]

Binding Affinity Annotations
ID	Source	Binding Affinity
NGA	Binding MOAD: 4OWK	Kd: 1.31e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.191
R-Value Work: 0.158
R-Value Observed: 0.159
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.389	α = 90
b = 79.832	β = 89.48
c = 148.694	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data scaling
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2014-05-28

Deposition Author(s):

Kaus, K.

Olson, R.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	1R15AI101977

Revision History (Full details and data files)

Version 1.0: 2014-05-28
Type: Initial release
Version 1.1: 2014-07-30
Changes: Database references
Version 1.2: 2015-02-25
Changes: Derived calculations
Version 1.3: 2015-10-07
Changes: Other
Version 1.4: 2017-09-27
Changes: Author supporting evidence, Derived calculations
Version 1.5: 2017-11-01
Changes: Derived calculations
Version 1.6: 2019-12-11
Changes: Author supporting evidence
Version 1.7: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.8: 2023-12-27
Changes: Data collection, Database references, Structure summary

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Help and Resources

4OWK

Crystal Structure of the Vibrio vulnificus Hemolysin/Cytolysin Beta-Trefoil Lectin with N-Acetyl-D-Galactosamine Bound

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)