8ZVT | pdb_00008zvt

Human citrate synthase intermediate 3

• PDB DOI: https://doi.org/10.2210/pdb8ZVT/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: 2.05 Å
• R-Value Free: 
  0.269 (Depositor), 0.272 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: experimental

Literature

Human citrate synthase intermediate 3

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: 49.75 kDa 
• Atom Count: 3,633 
• Modeled Residue Count: 434 
• Deposited Residue Count: 436 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Citrate synthase, mitochondrial	A	436	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
OAA	B [auth A]	OXALOACETATE ION C4 H3 O5 KHPXUQMNIQBQEV-UHFFFAOYSA-M
ACY	C [auth A]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.269 (Depositor), 0.272 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.84	α = 90
b = 57.84	β = 90
c = 250.36	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	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