7YH4 | pdb_00007yh4

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

PDB DOI: https://doi.org/10.2210/pdb7YH4/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-07-12 Released: 2023-08-02
Deposition Author(s): Chandravanshi, K., Gaur, N.K., Kumar, A., Makde, R.D.
Funding Organization(s): Department of Science & Technology (DST, India)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.03 Å
R-Value Free:
0.237 (Depositor), 0.236 (DCC)
R-Value Work:
0.197 (Depositor), 0.198 (DCC)
R-Value Observed:
0.199 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7YH4

This is version 1.2 of the entry. See complete history.

Literature

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

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

To be published.

Macromolecule Content

Total Structure Weight: 49.88 kDa
Atom Count: 3,140
Modeled Residue Count: 400
Deposited Residue Count: 454
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Xaa-Arg dipeptidase	A	454	Homo sapiens	Mutation(s): 0 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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8IYS1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.03 Å
R-Value Free: 0.237 (Depositor), 0.236 (DCC)
R-Value Work: 0.197 (Depositor), 0.198 (DCC)
R-Value Observed: 0.199 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.834	α = 90
b = 112.888	β = 90
c = 123.217	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-08-02

Deposition Author(s):

Chandravanshi, K.

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

Revision History (Full details and data files)

Version 1.0: 2023-08-02
Type: Initial release
Version 1.1: 2024-05-29
Changes: Data collection
Version 1.2: 2026-03-04
Changes: Refinement description, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.