5FQF

The details of glycolipid glycan hydrolysis by the structural analysis of a family 123 glycoside hydrolase from Clostridium perfringens

PDB DOI: https://doi.org/10.2210/pdb5FQF/pdb

Classification: HYDROLASE
Organism(s): Clostridium perfringens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-12-10 Released: 2016-03-30
Deposition Author(s): Noach, I., Pluvinage, B., Laurie, C., Abe, K.T., Alteen, M., Vocadlo, D.J., Boraston, A.B.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.198
R-Value Work: 0.147
R-Value Observed: 0.150

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 142.04 kDa
Atom Count: 10,495
Modelled Residue Count: 1,163
Deposited Residue Count: 1,220
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BETA-N-ACETYLGALACTOSAMINIDASE	A, B	610	Clostridium perfringens	Mutation(s): 0
UniProt
Find proteins for A0A0H2YNR7 (Clostridium perfringens (strain ATCC 13124 / DSM 756 / JCM 1290 / NCIMB 6125 / NCTC 8237 / Type A)) Explore A0A0H2YNR7 Go to UniProtKB: A0A0H2YNR7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0H2YNR7
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 M [auth B] SDF format, chain N [auth B] SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A]	C [auth A], D [auth A], M [auth B], N [auth B]	2-acetamido-2-deoxy-beta-D-galactopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-JAJWTYFOSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain M [auth B] Focus chain N [auth B]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain L [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain R [auth B] SDF format, chain T [auth B] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain Q [auth B] SDF format, chain S [auth B] SDF format, chain U [auth B] MOL2 format, chain E [auth A] MOL2 format, chain L [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain R [auth B] MOL2 format, chain T [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain S [auth B] MOL2 format, chain U [auth B]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.198
R-Value Work: 0.147
R-Value Observed: 0.150
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.03	α = 90
b = 114.79	β = 90
c = 134.7	γ = 90

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: 2016-03-30

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-03-30
Type: Initial release
Version 1.1: 2016-04-13
Changes: Database references
Version 1.2: 2016-04-20
Changes: Data collection
Version 1.3: 2016-08-24
Changes: Database references
Version 1.4: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Data collection, Derived calculations, Other, Structure summary
Version 1.5: 2024-01-10
Changes: Advisory, Data collection, Database references, Refinement description, Structure summary