8ZKJ | pdb_00008zkj

The crystal structure of apo-LDHC

• PDB DOI: https://doi.org/10.2210/pdb8ZKJ/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-05-16 Released: 2025-09-03 
• Deposition Author(s): Wu, C.Y., Wang, H.L.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free: 
  0.261 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.207 (DCC) 
• R-Value Observed: 
  0.212 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of human LDHC at 2.38 Angstroms resolution

Wu, C.Y., Wang, H.L.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 75.06 kDa 
• Atom Count: 5,073 
• Modeled Residue Count: 659 
• Deposited Residue Count: 682 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-lactate dehydrogenase C chain	A, B	341	Homo sapiens	Mutation(s): 0  Gene Names: LDHC, LDH3, LDHX EC: 1.1.1.27
UniProt & NIH Common Fund Data Resources
Find proteins for P07864 (Homo sapiens) Explore P07864  Go to UniProtKB:  P07864
PHAROS:  P07864 GTEx:  ENSG00000166796

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free:  0.261 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.207 (DCC) 
• R-Value Observed: 0.212 (Depositor) 

Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86	α = 90
b = 86	β = 90
c = 194.77	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-09-03 
Deposition Author(s): Wu, C.Y., Wang, H.L.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-09-03
  Type: Initial release