9JAV | pdb_00009jav

Crystal structure of NAD-dependent methanol dehydrogenase 2 from Bacillus methanolicus MGA3 in complex with NAD+

PDB DOI: https://doi.org/10.2210/pdb9JAV/pdb

Classification: OXIDOREDUCTASE
Organism(s): Bacillus methanolicus MGA3
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-08-25 Released: 2025-09-03
Deposition Author(s): Kong, X.D., Ma, B.D.
Funding Organization(s): Ministry of Science and Technology (MoST, China)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.240 (Depositor), 0.238 (DCC)
R-Value Work:
0.175 (Depositor), 0.177 (DCC)
R-Value Observed:
0.179 (Depositor)

Starting Model: in silico
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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

Crystal structure of NAD-dependent methanol dehydrogenase 2 from Bacillus methanolicus MGA3 in complex with NAD+

Kong, X.D., Ma, B.D.

To be published.

Macromolecule Content

Total Structure Weight: 425.09 kDa
Atom Count: 30,037
Modeled Residue Count: 3,840
Deposited Residue Count: 3,930
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD-dependent methanol dehydrogenase	A, B, C, D, E A, B, C, D, E, F, G, H, I, J	393	Bacillus methanolicus MGA3	Mutation(s): 0 Gene Names: mdh2, BMMGA3_03335 EC: 1.1.1.244
UniProt
Find proteins for I3E949 (Bacillus methanolicus (strain MGA3 / ATCC 53907)) Explore I3E949 Go to UniProtKB: I3E949
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	I3E949
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD (Subject of Investigation/LOI) Query on NAD Download Ideal Coordinates CCD File SDF format, chain Z [auth H] SDF format, chain V [auth F] SDF format, chain T [auth E] SDF format, chain R [auth D] SDF format, chain P [auth C] SDF format, chain N [auth B] SDF format, chain L [auth A] SDF format, chain DA [auth J] MOL2 format, chain Z [auth H] MOL2 format, chain V [auth F] MOL2 format, chain T [auth E] MOL2 format, chain R [auth D] MOL2 format, chain P [auth C] MOL2 format, chain N [auth B] MOL2 format, chain L [auth A] MOL2 format, chain DA [auth J] mmCIF format, chain Z [auth H] mmCIF format, chain V [auth F] mmCIF format, chain T [auth E] mmCIF format, chain R [auth D] mmCIF format, chain P [auth C] mmCIF format, chain N [auth B] mmCIF format, chain L [auth A] mmCIF format, chain DA [auth J]	DA [auth J] L [auth A] N [auth B] P [auth C] R [auth D] DA [auth J], L [auth A], N [auth B], P [auth C], R [auth D], T [auth E], V [auth F], Z [auth H]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain DA [auth J] Focus chain L [auth A] Focus chain N [auth B] Focus chain P [auth C] Focus chain R [auth D] Focus chain T [auth E] Focus chain V [auth F] Focus chain Z [auth H] Interactions & Density Focus chain DA [auth J] Focus chain L [auth A] Focus chain N [auth B] Focus chain P [auth C] Focus chain R [auth D] Focus chain T [auth E] Focus chain V [auth F] Focus chain Z [auth H]
APR (Subject of Investigation/LOI) Query on APR Download Ideal Coordinates CCD File SDF format, chain X [auth G] SDF format, chain BA [auth I] MOL2 format, chain X [auth G] MOL2 format, chain BA [auth I] mmCIF format, chain X [auth G] mmCIF format, chain BA [auth I]	BA [auth I], X [auth G]	ADENOSINE-5-DIPHOSPHORIBOSE C₁₅ H₂₃ N₅ O₁₄ P₂ SRNWOUGRCWSEMX-KEOHHSTQSA-N		Interactions Focus chain BA [auth I] Focus chain X [auth G] Interactions & Density Focus chain BA [auth I] Focus chain X [auth G]
MN (Subject of Investigation/LOI) Query on MN Download Ideal Coordinates CCD File SDF format, chain Y [auth H] SDF format, chain W [auth G] SDF format, chain U [auth F] SDF format, chain S [auth E] SDF format, chain Q [auth D] SDF format, chain O [auth C] SDF format, chain M [auth B] SDF format, chain K [auth A] SDF format, chain CA [auth J] SDF format, chain AA [auth I] MOL2 format, chain Y [auth H] MOL2 format, chain W [auth G] MOL2 format, chain U [auth F] MOL2 format, chain S [auth E] MOL2 format, chain Q [auth D] MOL2 format, chain O [auth C] MOL2 format, chain M [auth B] MOL2 format, chain K [auth A] MOL2 format, chain CA [auth J] MOL2 format, chain AA [auth I] mmCIF format, chain Y [auth H] mmCIF format, chain W [auth G] mmCIF format, chain U [auth F] mmCIF format, chain S [auth E] mmCIF format, chain Q [auth D] mmCIF format, chain O [auth C] mmCIF format, chain M [auth B] mmCIF format, chain K [auth A] mmCIF format, chain CA [auth J] mmCIF format, chain AA [auth I]	AA [auth I] CA [auth J] K [auth A] M [auth B] O [auth C] AA [auth I], CA [auth J], K [auth A], M [auth B], O [auth C], Q [auth D], S [auth E], U [auth F], W [auth G], Y [auth H]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain AA [auth I] Focus chain CA [auth J] Focus chain K [auth A] Focus chain M [auth B] Focus chain O [auth C] Focus chain Q [auth D] Focus chain S [auth E] Focus chain U [auth F] Focus chain W [auth G] Focus chain Y [auth H] Interactions & Density Focus chain AA [auth I] Focus chain CA [auth J] Focus chain K [auth A] Focus chain M [auth B] Focus chain O [auth C] Focus chain Q [auth D] Focus chain S [auth E] Focus chain U [auth F] Focus chain W [auth G] Focus chain Y [auth H]