8ZIK | pdb_00008zik

Crystal structure of a beta-1,4-endoglucanase from Bispora sp. MEY-1 in complex with cellotetraose

PDB DOI: https://doi.org/10.2210/pdb8ZIK/pdb

Classification: HYDROLASE
Organism(s): Bispora sp. MEY-1
Expression System: Komagataella pastoris
Mutation(s): Yes

Deposited: 2024-05-14 Released: 2025-05-21
Deposition Author(s): Zheng, J., Luo, H.Y., Yao, B., Tian, J.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.87 Å
R-Value Free:
0.239 (Depositor), 0.239 (DCC)
R-Value Work:
0.188 (Depositor), 0.189 (DCC)
R-Value Observed:
0.191 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Unraveling the Key Determinants of Substrate Promiscuity in Glycoside Hydrolase Family 5_5 Cellulases

Zheng, J., Luo, H.Y.

To be published.

Macromolecule Content

Total Structure Weight: 149.38 kDa
Atom Count: 10,954
Modeled Residue Count: 1,228
Deposited Residue Count: 1,288
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cellulase	A [auth D], B, C [auth A], D [auth C]	322	Bispora sp. MEY-1	Mutation(s): 2 Gene Names: M433DRAFT_60941 EC: 3.2.1.4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Glycosylation
Glycosylation Sites: 5	Glycosylation Focus chain A [auth D] Focus chain B Focus chain C [auth A] Focus chain D [auth C]
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose	E, F, G, H, I E, F, G, H, I, J	4		N/A	Interactions Focus chain E Focus chain F Focus chain G Focus chain H Focus chain I Focus chain J Interactions & Density Focus chain E Focus chain F Focus chain G Focus chain H Focus chain I Focus chain J
Glycosylation Resources
GlyTouCan: G00025MO GlyCosmos: G00025MO GlyGen: G00025MO

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain L [auth D] SDF format, chain M [auth D] SDF format, chain N [auth D] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain W [auth C] SDF format, chain X [auth C] SDF format, chain Y [auth C] SDF format, chain Z [auth C] SDF format, chain K [auth D] MOL2 format, chain AA [auth C] MOL2 format, chain L [auth D] MOL2 format, chain M [auth D] MOL2 format, chain N [auth D] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] MOL2 format, chain K [auth D] mmCIF format, chain AA [auth C] mmCIF format, chain L [auth D] mmCIF format, chain M [auth D] mmCIF format, chain N [auth D] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A] mmCIF format, chain U [auth A] mmCIF format, chain V [auth A] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth C] mmCIF format, chain K [auth D]	AA [auth C] K [auth D] L [auth D] M [auth D] N [auth D] AA [auth C], K [auth D], L [auth D], M [auth D], N [auth D], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth A], T [auth A], U [auth A], V [auth A], W [auth C], X [auth C], Y [auth C], Z [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth C] Focus chain K [auth D] Focus chain L [auth D] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain K [auth D] Focus chain L [auth D] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C]