6YOZ

HiCel7B labelled with b-1,4-glucosyl cyclophellitol

PDB DOI: https://doi.org/10.2210/pdb6YOZ/pdb

Classification: HYDROLASE
Organism(s): Humicola insolens
Expression System: Aspergillus oryzae
Mutation(s): No

Deposited: 2020-04-15 Released: 2020-09-16
Deposition Author(s): McGregor, N.G.S., Davies, G.J.
Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.88 Å
R-Value Free: 0.236
R-Value Work: 0.202

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: 91.86 kDa
Atom Count: 6,811
Modelled Residue Count: 798
Deposited Residue Count: 800
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endoglucanase 1	A [auth AAA], B [auth BBB]	400	Humicola insolens	Mutation(s): 0 Gene Names: CEL7B EC: 3.2.1.4
UniProt
Find proteins for P56680 (Humicola insolens) Explore P56680 Go to UniProtKB: P56680
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P56680
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain C [auth AAA] SDF format, chain D [auth AAA] SDF format, chain O [auth BBB] SDF format, chain U [auth BBB] MOL2 format, chain C [auth AAA] MOL2 format, chain D [auth AAA] MOL2 format, chain O [auth BBB] MOL2 format, chain U [auth BBB]	C [auth AAA], D [auth AAA], O [auth BBB], U [auth BBB]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain C [auth AAA] Focus chain D [auth AAA] Focus chain O [auth BBB] Focus chain U [auth BBB] Interactions & Density Focus chain C [auth AAA] Focus chain D [auth AAA] Focus chain O [auth BBB] Focus chain U [auth BBB]
YLL (Subject of Investigation/LOI) Query on YLL Download Ideal Coordinates CCD File SDF format, chain I [auth AAA] SDF format, chain W [auth BBB] MOL2 format, chain I [auth AAA] MOL2 format, chain W [auth BBB]	I [auth AAA], W [auth BBB]	(1R,2S,3S,4S,5R,6R)-6-(HYDROXYMETHYL)CYCLOHEXANE-1,2,3,4,5-PENTOL C₇ H₁₄ O₆ QFYQIWDMMSKNFF-NYLBLOMBSA-N		Interactions Focus chain I [auth AAA] Focus chain W [auth BBB] Interactions & Density Focus chain I [auth AAA] Focus chain W [auth BBB]
BGC Query on BGC Download Ideal Coordinates CCD File SDF format, chain H [auth AAA] SDF format, chain V [auth BBB] MOL2 format, chain H [auth AAA] MOL2 format, chain V [auth BBB]	H [auth AAA], V [auth BBB]	beta-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-VFUOTHLCSA-N		Interactions Focus chain H [auth AAA] Focus chain V [auth BBB] Interactions & Density Focus chain H [auth AAA] Focus chain V [auth BBB]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth AAA] SDF format, chain F [auth AAA] SDF format, chain G [auth AAA] SDF format, chain L [auth AAA] SDF format, chain N [auth AAA] SDF format, chain P [auth BBB] SDF format, chain Q [auth BBB] SDF format, chain R [auth BBB] SDF format, chain S [auth BBB] SDF format, chain T [auth BBB] SDF format, chain X [auth BBB] SDF format, chain Z [auth BBB] MOL2 format, chain E [auth AAA] MOL2 format, chain F [auth AAA] MOL2 format, chain G [auth AAA] MOL2 format, chain L [auth AAA] MOL2 format, chain N [auth AAA] MOL2 format, chain P [auth BBB] MOL2 format, chain Q [auth BBB] MOL2 format, chain R [auth BBB] MOL2 format, chain S [auth BBB] MOL2 format, chain T [auth BBB] MOL2 format, chain X [auth BBB] MOL2 format, chain Z [auth BBB]	E [auth AAA] F [auth AAA] G [auth AAA] L [auth AAA] N [auth AAA] E [auth AAA], F [auth AAA], G [auth AAA], L [auth AAA], N [auth AAA], P [auth BBB], Q [auth BBB], R [auth BBB], S [auth BBB], T [auth BBB], X [auth BBB], Z [auth BBB]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth AAA] Focus chain F [auth AAA] Focus chain G [auth AAA] Focus chain L [auth AAA] Focus chain N [auth AAA] Focus chain P [auth BBB] Focus chain Q [auth BBB] Focus chain R [auth BBB] Focus chain S [auth BBB] Focus chain T [auth BBB] Focus chain X [auth BBB] Focus chain Z [auth BBB] Interactions & Density Focus chain E [auth AAA] Focus chain F [auth AAA] Focus chain G [auth AAA] Focus chain L [auth AAA] Focus chain N [auth AAA] Focus chain P [auth BBB] Focus chain Q [auth BBB] Focus chain R [auth BBB] Focus chain S [auth BBB] Focus chain T [auth BBB] Focus chain X [auth BBB] Focus chain Z [auth BBB]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain J [auth AAA] SDF format, chain K [auth AAA] SDF format, chain Y [auth BBB] MOL2 format, chain J [auth AAA] MOL2 format, chain K [auth AAA] MOL2 format, chain Y [auth BBB]	J [auth AAA], K [auth AAA], Y [auth BBB]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain J [auth AAA] Focus chain K [auth AAA] Focus chain Y [auth BBB] Interactions & Density Focus chain J [auth AAA] Focus chain K [auth AAA] Focus chain Y [auth BBB]
ACM Query on ACM Download Ideal Coordinates CCD File SDF format, chain M [auth AAA] MOL2 format, chain M [auth AAA]	M [auth AAA]	ACETAMIDE C₂ H₅ N O DLFVBJFMPXGRIB-UHFFFAOYSA-N		Interactions Focus chain M [auth AAA] Interactions & Density Focus chain M [auth AAA]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA Query on PCA	A [auth AAA], B [auth BBB]	L-PEPTIDE LINKING	C₅ H₇ N O₃		GLN

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.88 Å
R-Value Free: 0.236
R-Value Work: 0.202
Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102	α = 90
b = 102	β = 90
c = 278.85	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2020-09-16

Deposition Author(s):

McGregor, N.G.S.

Davies, G.J.

Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/R001162/1

Revision History (Full details and data files)

Version 1.0: 2020-09-16
Type: Initial release
Version 1.1: 2021-09-29
Changes: Data collection, Database references
Version 1.2: 2021-10-13
Changes: Advisory, Data collection, Database references, Derived calculations, Source and taxonomy
Version 1.3: 2024-01-24
Changes: Data collection, Derived calculations, Refinement description