8ZEL | pdb_00008zel

Crystal structure of human cytosolic beta-alanyl lysine dipeptidase Tyr314Phe mutant with a crystal soaked in beta-alanyl ornithine

• PDB DOI: https://doi.org/10.2210/pdb8ZEL/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2024-05-06 Released: 2025-05-14 
• Deposition Author(s): Chandravanshi, K., Kumar, A., Makde, R.D.
• Funding Organization(s): Department of Science & Technology (DST, India)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.232 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of human cytosolic beta-alanyl lysine dipeptidase Tyr314Phe mutant with a crystal soaked in beta-alanyl ornithine

Chandravanshi, K., Kumar, A., Makde, R.D.

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.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 50.18 kDa 
• Atom Count: 3,147 
• Modeled Residue Count: 400 
• Deposited Residue Count: 454 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Xaa-Arg dipeptidase	A	454	Homo sapiens	Mutation(s): 1  Gene Names: PM20D2, ACY1L2 EC: 3.4.13.4
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IYS1 (Homo sapiens) Explore Q8IYS1  Go to UniProtKB:  Q8IYS1
PHAROS:  Q8IYS1 GTEx:  ENSG00000146281

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ORN (Subject of Investigation/LOI)	D [auth A]	L-ornithine C5 H12 N2 O2 AHLPHDHHMVZTML-BYPYZUCNSA-N
TRS	E [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
ZN	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACY	F [auth A]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.232 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.777	α = 90
b = 112.894	β = 90
c = 123.255	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: 2025-05-14 
Deposition Author(s): Chandravanshi, K., Kumar, A., Makde, R.D.

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Funding Organization	Location	Grant Number
Department of Science & Technology (DST, India)	India	IF190153

Revision History  

• Version 1.0: 2025-05-14
  Type: Initial release