9KHN | pdb_00009khn

Crystal structure of human cystathionine gamma-lyase in complex with L-aminoethoxyvinylglycine

• PDB DOI: https://doi.org/10.2210/pdb9KHN/pdb

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


• Deposited: 2024-11-10 Released: 2025-11-12 
• Deposition Author(s): Kukimoto-Niino, M., Shirouzu, M.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.215 (Depositor), 0.217 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.172 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of human cystathionine gamma-lyase in complex with L-aminoethoxyvinylglycine

Kukimoto-Niino, M., Shirouzu, M., Honda, K.

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)

Macromolecule Content 

• Total Structure Weight: 178.9 kDa 
• Atom Count: 13,215 
• Modeled Residue Count: 1,562 
• Deposited Residue Count: 1,612 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cystathionine gamma-lyase	A, B, C, D	403	Homo sapiens	Mutation(s): 0  Gene Names: CTH EC: 4.4.1.1 (PDB Primary Data), 4.4.1.2 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P32929 (Homo sapiens) Explore P32929  Go to UniProtKB:  P32929
PHAROS:  P32929 GTEx:  ENSG00000116761

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PPG (Subject of Investigation/LOI)	E [auth A], F [auth B], G [auth C], H [auth D]	(2E,3E)-4-(2-aminoethoxy)-2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)imino]but-3-enoic acid C14 H20 N3 O8 P OBCQKAZQAHYUOZ-CALQLVRRSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.215 (Depositor), 0.217 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.172 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.214	α = 90
b = 151.711	β = 110.94
c = 83.524	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-12 
Deposition Author(s): Kukimoto-Niino, M., Shirouzu, M.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-11-12
  Type: Initial release