5GWF

FraC with GlcNAc(6S) bound

PDB DOI: https://doi.org/10.2210/pdb5GWF/pdb

Classification: TOXIN
Organism(s): Actinia fragacea
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-09-11 Released: 2017-06-21
Deposition Author(s): Caaveiro, J.M.M., Tsumoto, K.
Funding Organization(s): JSPS

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.163
R-Value Work: 0.118
R-Value Observed: 0.119

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: 80.76 kDa
Atom Count: 6,526
Modelled Residue Count: 708
Deposited Residue Count: 720
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DELTA-actitoxin-Afr1a	A, B, C, D	180	Actinia fragacea	Mutation(s): 0
UniProt
Find proteins for B9W5G6 (Actinia fragacea) Explore B9W5G6 Go to UniProtKB: B9W5G6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B9W5G6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NGY Query on NGY Download Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain R [auth D] MOL2 format, chain F [auth B] MOL2 format, chain R [auth D]	F [auth B], R [auth D]	2-acetamido-2-deoxy-6-O-sulfo-alpha-D-glucopyranose C₈ H₁₅ N O₉ S WJFVEEAIYIOATH-PVFLNQBWSA-N		Interactions Focus chain F [auth B] Focus chain R [auth D] Interactions & Density Focus chain F [auth B] Focus chain R [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain Q [auth C] MOL2 format, chain M [auth B] MOL2 format, chain Q [auth C]	M [auth B], Q [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain M [auth B] Focus chain Q [auth C] Interactions & Density Focus chain M [auth B] Focus chain Q [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain O [auth C] SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain N [auth C] SDF format, chain P [auth C] SDF format, chain S [auth D] SDF format, chain T [auth D] SDF format, chain U [auth D] MOL2 format, chain L [auth B] MOL2 format, chain O [auth C] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain N [auth C] MOL2 format, chain P [auth C] MOL2 format, chain S [auth D] MOL2 format, chain T [auth D] MOL2 format, chain U [auth D]	E [auth A] G [auth B] H [auth B] I [auth B] J [auth B] E [auth A], G [auth B], H [auth B], I [auth B], J [auth B], K [auth B], L [auth B], N [auth C], O [auth C], P [auth C], S [auth D], T [auth D], U [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.163
R-Value Work: 0.118
R-Value Observed: 0.119
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.16	α = 90
b = 44.4	β = 92.76
c = 114.36	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2017-06-21

Deposition Author(s):

Caaveiro, J.M.M.

Tsumoto, K.

Funding Organization	Location	Grant Number
JSPS	Japan	25249115
JSPS	Japan	15K06962

Revision History (Full details and data files)

Version 1.0: 2017-06-21
Type: Initial release
Version 1.1: 2017-12-06
Changes: Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-11-08
Changes: Data collection, Database references, Refinement description, Structure summary

Prepare Data

Validate Data

Deposit Data

Help and Resources

5GWF

FraC with GlcNAc(6S) bound

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)