9IOV | pdb_00009iov

Gossypol bound lactate dehydrogenase A

PDB DOI: https://doi.org/10.2210/pdb9IOV/pdb

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

Deposited: 2024-07-09 Released: 2025-07-09
Deposition Author(s): Ha, M.S., Han, C.W., Jeong, M.S., Jang, S.B.
Funding Organization(s): National Research Foundation (NRF, Korea)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.98 Å
R-Value Free:
0.273 (Depositor), 0.279 (DCC)
R-Value Work:
0.238 (Depositor), 0.244 (DCC)
R-Value Observed:
0.240 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Gossypol bound lactate dehydrogenase A

Ha, M.S., Han, C.W., Jeong, M.S., Jang, S.B.

To be published.

Macromolecule Content

Total Structure Weight: 879 kDa
Atom Count: 61,670
Modeled Residue Count: 7,944
Deposited Residue Count: 7,944
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-lactate dehydrogenase A chain	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X	331	Homo sapiens	Mutation(s): 0 Gene Names: LDHA, PIG19 EC: 1.1.1.27
UniProt & NIH Common Fund Data Resources
Find proteins for P00338 (Homo sapiens) Explore P00338 Go to UniProtKB: P00338
PHAROS: P00338 GTEx: ENSG00000134333
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00338
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GO3 (Subject of Investigation/LOI) Query on GO3 Download Ideal Coordinates CCD File SDF format, chain Y [auth Q] MOL2 format, chain Y [auth Q] mmCIF format, chain Y [auth Q]	Y [auth Q]	Gossypol C₃₀ H₃₀ O₈ QBKSWRVVCFFDOT-UHFFFAOYSA-N		Interactions Focus chain Y [auth Q] Interactions & Density Focus chain Y [auth Q]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.98 Å
R-Value Free: 0.273 (Depositor), 0.279 (DCC)
R-Value Work: 0.238 (Depositor), 0.244 (DCC)
R-Value Observed: 0.240 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.369	α = 89.98
b = 110.924	β = 90.04
c = 217.546	γ = 88.37

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
HKL-2000	data reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-07-09

Deposition Author(s):

Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	--

Revision History (Full details and data files)

Version 1.0: 2025-07-09
Type: Initial release

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.