8XZC | pdb_00008xzc

Crystal structure of human cytosolic beta-alanyl lysine dipeptidase (PM20D2) Tyr314Phe mutant

• PDB DOI: https://doi.org/10.2210/pdb8XZC/pdb

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


• Deposited: 2024-01-21 Released: 2025-01-22 
• 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: 2.35 Å
• R-Value Free: 
  0.240 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of human cytosolic beta-alanyl lysine dipeptidase (PM20D2) Tyr314Phe mutant

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 and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 50.05 kDa 
• Atom Count: 3,120 
• Modeled Residue Count: 401 
• 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4 (Subject of Investigation/LOI)	B [auth A], C [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
ZN (Subject of Investigation/LOI)	D [auth A], E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free:  0.240 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.935	α = 90
b = 115.526	β = 90
c = 124.434	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: 2025-01-22 
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	--

Revision History  

• Version 1.0: 2025-01-22
  Type: Initial release