8HMN | pdb_00008hmn

Crystal structure of GAPDH complexed with arsenate from Lactiplantibacillus plantarum

PDB DOI: https://doi.org/10.2210/pdb8HMN/pdb

Classification: OXIDOREDUCTASE
Organism(s): Lactiplantibacillus plantarum
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-12-05 Released: 2023-12-06
Deposition Author(s): Yoneda, K., Kinoshita, H.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.16 Å
R-Value Free:
0.261 (Depositor), 0.268 (DCC)
R-Value Work:
0.216 (Depositor), 0.225 (DCC)
R-Value Observed:
0.218 (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

Crystal structure of GAPDH complexed with arsenate from Lactiplantibacillus plantarum

Yoneda, K., Kinoshita, H.

To be published.

Macromolecule Content

Total Structure Weight: 158.17 kDa
Atom Count: 11,007
Modeled Residue Count: 1,320
Deposited Residue Count: 1,440
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyceraldehyde-3-phosphate dehydrogenase	A, B, C, D	360	Lactiplantibacillus plantarum	Mutation(s): 0 Gene Names: gap
UniProt
Find proteins for Q88YH6 (Lactiplantibacillus plantarum) Explore Q88YH6 Go to UniProtKB: Q88YH6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q88YH6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 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 I [auth B] SDF format, chain L [auth C] SDF format, chain O [auth D] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain L [auth C] MOL2 format, chain O [auth D] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain L [auth C] mmCIF format, chain O [auth D]	E [auth A], I [auth B], L [auth C], O [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain O [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain O [auth D]
ART (Subject of Investigation/LOI) Query on ART Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain P [auth D] SDF format, chain M [auth C] SDF format, chain J [auth B] MOL2 format, chain F [auth A] MOL2 format, chain P [auth D] MOL2 format, chain M [auth C] MOL2 format, chain J [auth B] mmCIF format, chain F [auth A] mmCIF format, chain P [auth D] mmCIF format, chain M [auth C] mmCIF format, chain J [auth B]	F [auth A], J [auth B], M [auth C], P [auth D]	ARSENATE As O₄ DJHGAFSJWGLOIV-UHFFFAOYSA-K		Interactions Focus chain F [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D] Interactions & Density Focus chain F [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D]
TRS Query on TRS 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]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain Q [auth D] SDF format, chain N [auth C] SDF format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain Q [auth D] MOL2 format, chain N [auth C] MOL2 format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain Q [auth D] mmCIF format, chain N [auth C] mmCIF format, chain G [auth A]	G [auth A], K [auth B], N [auth C], Q [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain Q [auth D] Interactions & Density Focus chain G [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain Q [auth D]