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), 0.240 (DCC)
R-Value Work:
0.197 (Depositor), 0.200 (DCC)
R-Value Observed:
0.199 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.1 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:

(by identity cutoff) | 3D Structure

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% Identity50% Identity70% Identity90% Identity95% Identity100% 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 B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [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), 0.240 (DCC)
R-Value Work: 0.197 (Depositor), 0.200 (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

View Full Validation Report

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

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.