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
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wwPDB Validation 3D Report Full Report

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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

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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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

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Ligand Structure Quality Assessment

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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

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.