7YA4

Formate dehydrogenase from Novosphingobium sp. AP12 with NAD and Azide

PDB DOI: https://doi.org/10.2210/pdb7YA4/pdb

Classification: OXIDOREDUCTASE
Organism(s): Novosphingobium sp. AP12
Expression System: Escherichia coli K-12
Mutation(s): No

Deposited: 2022-06-27 Released: 2023-07-12
Deposition Author(s): Kim, S., Kim, K.-J.
Funding Organization(s): Ministry of Science, ICT and Future Planning (MSIP)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.191
R-Value Work: 0.155

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Dual cofactor specific formate dehydrogenase from Novosphingobium sp. AP12 with high activity.

Kim, S., Kim, K.-J.

To be published.

Macromolecule Content

Total Structure Weight: 176.15 kDa
Atom Count: 12,896
Modelled Residue Count: 1,517
Deposited Residue Count: 1,568
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Formate dehydrogenase	A, B, C, D	392	Novosphingobium sp. AP12	Mutation(s): 0 Gene Names: PMI02_01157 EC: 1.17.1.9
UniProt
Find proteins for J2HCX1 (Novosphingobium sp. AP12) Explore J2HCX1 Go to UniProtKB: J2HCX1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	J2HCX1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 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 E [auth A] SDF format, chain K [auth B] MOL2 format, chain E [auth A] MOL2 format, chain K [auth B] mmCIF format, chain E [auth A] mmCIF format, chain K [auth B]	E [auth A], K [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain K [auth B] Interactions & Density Focus chain E [auth A] Focus chain K [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain M [auth B] SDF format, chain N [auth C] SDF format, chain P [auth D] MOL2 format, chain J [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth C] MOL2 format, chain P [auth D] mmCIF format, chain J [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth C] mmCIF format, chain P [auth D]	J [auth A], M [auth B], N [auth C], P [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain M [auth B] Focus chain N [auth C] Focus chain P [auth D] Interactions & Density Focus chain J [auth A] Focus chain M [auth B] Focus chain N [auth C] Focus chain P [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain O [auth C] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain O [auth C] mmCIF format, chain G [auth A] mmCIF format, chain I [auth A] mmCIF format, chain O [auth C]	G [auth A], I [auth A], O [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain I [auth A] Focus chain O [auth C] Interactions & Density Focus chain G [auth A] Focus chain I [auth A] Focus chain O [auth C]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain Q [auth D] MOL2 format, chain Q [auth D] mmCIF format, chain Q [auth D]	Q [auth D]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain Q [auth D] Interactions & Density Focus chain Q [auth D]
AZI (Subject of Investigation/LOI) Query on AZI Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain L [auth B] MOL2 format, chain F [auth A] MOL2 format, chain L [auth B] mmCIF format, chain F [auth A] mmCIF format, chain L [auth B]	F [auth A], L [auth B]	AZIDE ION N₃ IVRMZWNICZWHMI-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain L [auth B] Interactions & Density Focus chain F [auth A] Focus chain L [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]