8ZVU | pdb_00008zvu

Human citrate synthase intermediate 4

• PDB DOI: https://doi.org/10.2210/pdb8ZVU/pdb

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


• Deposited: 2024-06-12 Released: 2025-06-18 
• Deposition Author(s): Yang, L.Y., Fang, Y.J.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 
  0.233 (Depositor), 0.236 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: experimental

Literature

Human citrate synthase intermediate 4

Yang, L.Y., Fang, Y.J.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 98.36 kDa 
• Atom Count: 7,252 
• Modeled Residue Count: 868 
• Deposited Residue Count: 868 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Citrate synthase, mitochondrial	A, B	434	Homo sapiens	Mutation(s): 0  Gene Names: CS EC: 2.3.3.1
UniProt & NIH Common Fund Data Resources
Find proteins for O75390 (Homo sapiens) Explore O75390  Go to UniProtKB:  O75390
PHAROS:  O75390 GTEx:  ENSG00000062485

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
COA	D [auth A]	COENZYME A C21 H36 N7 O16 P3 S RGJOEKWQDUBAIZ-IBOSZNHHSA-N
CIT	C [auth A]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
OAA	E [auth B]	OXALOACETATE ION C4 H3 O5 KHPXUQMNIQBQEV-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free:  0.233 (Depositor), 0.236 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.912	α = 101.45
b = 59.689	β = 98.91
c = 73.434	γ = 116.47

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-06-18 
Deposition Author(s): Yang, L.Y., Fang, Y.J.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2025-06-18
  Type: Initial release