9U4X | pdb_00009u4x

Crystal Structure of Alcohol Dehydrogenase from Anoxybacillus geothermalis D9

PDB DOI: https://doi.org/10.2210/pdb9U4X/pdb

Classification: OXIDOREDUCTASE
Organism(s): Anoxybacteroides rupiense
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-03-20 Released: 2026-03-25
Deposition Author(s): Riem, E.A.A., Kamarudin, N.H.A., Ali, M.S.M., Noor, N.D.M.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.241 (Depositor), 0.241 (DCC)
R-Value Work:
0.200 (Depositor), 0.200 (DCC)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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

Literature

Alcohol Dehydrogenase from Anoxybacillus geothermalis D9

Riem, E.A.A., Kamarudin, N.H.A., Ali, M.S.M., Noor, N.D.M.

To be published.

Macromolecule Content

Total Structure Weight: 289.79 kDa
Atom Count: 20,398
Modeled Residue Count: 2,696
Deposited Residue Count: 2,696
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alcohol dehydrogenase	A, B, C, D, E A, B, C, D, E, F, G, H	337	Anoxybacteroides rupiense	Mutation(s): 0 EC: 1.1.1.1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth C] SDF format, chain N [auth C] SDF format, chain O [auth D] SDF format, chain P [auth D] SDF format, chain Q [auth E] SDF format, chain R [auth E] SDF format, chain S [auth F] SDF format, chain T [auth F] SDF format, chain U [auth G] SDF format, chain V [auth G] SDF format, chain W [auth H] SDF format, chain X [auth H] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] MOL2 format, chain O [auth D] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth E] MOL2 format, chain R [auth E] MOL2 format, chain S [auth F] MOL2 format, chain T [auth F] MOL2 format, chain U [auth G] MOL2 format, chain V [auth G] MOL2 format, chain W [auth H] MOL2 format, chain X [auth H] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth C] mmCIF format, chain N [auth C] mmCIF format, chain O [auth D] mmCIF format, chain P [auth D] mmCIF format, chain Q [auth E] mmCIF format, chain R [auth E] mmCIF format, chain S [auth F] mmCIF format, chain T [auth F] mmCIF format, chain U [auth G] mmCIF format, chain V [auth G] mmCIF format, chain W [auth H] mmCIF format, chain X [auth H]	I [auth A] J [auth A] K [auth B] L [auth B] M [auth C] I [auth A], J [auth A], K [auth B], L [auth B], M [auth C], N [auth C], O [auth D], P [auth D], Q [auth E], R [auth E], S [auth F], T [auth F], U [auth G], V [auth G], W [auth H], X [auth H]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth E] Focus chain R [auth E] Focus chain S [auth F] Focus chain T [auth F] Focus chain U [auth G] Focus chain V [auth G] Focus chain W [auth H] Focus chain X [auth H] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth E] Focus chain R [auth E] Focus chain S [auth F] Focus chain T [auth F] Focus chain U [auth G] Focus chain V [auth G] Focus chain W [auth H] Focus chain X [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.241 (Depositor), 0.241 (DCC)
R-Value Work: 0.200 (Depositor), 0.200 (DCC)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.607	α = 90
b = 130.769	β = 90.704
c = 134.918	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-03-25

Deposition Author(s):

Kamarudin, N.H.A.

Funding Organization	Location	Grant Number
Other government	Japan	2023B6876

Revision History (Full details and data files)

Version 1.0: 2026-03-25
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.