8QDE | pdb_00008qde

Crystal structure of a truncated human L-Lactate Dehydrogenase B protein in complex with NADH and oxamate

PDB DOI: https://doi.org/10.2210/pdb8QDE/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-08-29 Released: 2024-09-11
Deposition Author(s): Van Gysel, M., Wouters, J.
Funding Organization(s): Fonds National de la Recherche Scientifique (FNRS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.98 Å
R-Value Free:
0.310 (Depositor), 0.311 (DCC)
R-Value Work:
0.231 (Depositor), 0.231 (DCC)
R-Value Observed:
0.235 (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 a truncated human L-Lactate Dehydrogenase B protein in complex with NADH and oxamate

Van Gysel, M., Wouters, J.

To be published.

Macromolecule Content

Total Structure Weight: 150.68 kDa
Atom Count: 10,081
Modeled Residue Count: 1,254
Deposited Residue Count: 1,320
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-lactate dehydrogenase B chain	A, B, C, D	330	Homo sapiens	Mutation(s): 0 Gene Names: LDHB EC: 1.1.1.27
UniProt & NIH Common Fund Data Resources
Find proteins for P07195 (Homo sapiens) Explore P07195 Go to UniProtKB: P07195
PHAROS: P07195 GTEx: ENSG00000111716
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P07195
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAI (Subject of Investigation/LOI) Query on NAI Download Ideal Coordinates CCD File SDF format, chain U [auth D] SDF format, chain P [auth C] SDF format, chain K [auth B] SDF format, chain E [auth A] MOL2 format, chain U [auth D] MOL2 format, chain P [auth C] MOL2 format, chain K [auth B] MOL2 format, chain E [auth A] mmCIF format, chain U [auth D] mmCIF format, chain P [auth C] mmCIF format, chain K [auth B] mmCIF format, chain E [auth A]	E [auth A], K [auth B], P [auth C], U [auth D]	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE C₂₁ H₂₉ N₇ O₁₄ P₂ BOPGDPNILDQYTO-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain K [auth B] Focus chain P [auth C] Focus chain U [auth D] Interactions & Density Focus chain E [auth A] Focus chain K [auth B] Focus chain P [auth C] Focus chain U [auth D]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain R [auth C] SDF format, chain N [auth B] SDF format, chain G [auth A] MOL2 format, chain R [auth C] MOL2 format, chain N [auth B] MOL2 format, chain G [auth A] mmCIF format, chain R [auth C] mmCIF format, chain N [auth B] mmCIF format, chain G [auth A]	G [auth A], N [auth B], R [auth C]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain N [auth B] Focus chain R [auth C] Interactions & Density Focus chain G [auth A] Focus chain N [auth B] Focus chain R [auth C]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain M [auth B] MOL2 format, chain M [auth B] mmCIF format, chain M [auth B]	M [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain M [auth B] Interactions & Density Focus chain M [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain W [auth D] SDF format, chain T [auth C] SDF format, chain S [auth C] SDF format, chain O [auth B] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain W [auth D] MOL2 format, chain T [auth C] MOL2 format, chain S [auth C] MOL2 format, chain O [auth B] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain W [auth D] mmCIF format, chain T [auth C] mmCIF format, chain S [auth C] mmCIF format, chain O [auth B] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A] I [auth A] J [auth A] O [auth B] S [auth C] H [auth A], I [auth A], J [auth A], O [auth B], S [auth C], T [auth C], W [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain O [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain W [auth D] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain O [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain W [auth D]
OXM (Subject of Investigation/LOI) Query on OXM Download Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain Q [auth C] SDF format, chain V [auth D] SDF format, chain F [auth A] MOL2 format, chain L [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain V [auth D] MOL2 format, chain F [auth A] mmCIF format, chain L [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain V [auth D] mmCIF format, chain F [auth A]	F [auth A], L [auth B], Q [auth C], V [auth D]	OXAMIC ACID C₂ H₃ N O₃ SOWBFZRMHSNYGE-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain L [auth B] Focus chain Q [auth C] Focus chain V [auth D] Interactions & Density Focus chain F [auth A] Focus chain L [auth B] Focus chain Q [auth C] Focus chain V [auth D]