8ZEI | pdb_00008zei

Crystal structure of human cytosolic beta-alanyl lysine dipeptidase with crystal soaked in beta-alanyl histidine

PDB DOI: https://doi.org/10.2210/pdb8ZEI/pdb

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

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.219 (Depositor), 0.219 (DCC)
R-Value Work:
0.203 (Depositor), 0.203 (DCC)
R-Value Observed:
0.203 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of human cytosolic beta-alanyl lysine dipeptidase with crystal soaked in beta-alanyl histidine

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

To be published.

Macromolecule Content

Total Structure Weight: 50.3 kDa
Atom Count: 3,155
Modeled Residue Count: 401
Deposited Residue Count: 454
Unique protein chains: 1

Macromolecules

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(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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HIS (Subject of Investigation/LOI) Query on HIS Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	HISTIDINE C₆ H₁₀ N₃ O₂ HNDVDQJCIGZPNO-YFKPBYRVSA-O		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
TRS (Subject of Investigation/LOI) Query on TRS Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
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]
ACY (Subject of Investigation/LOI) Query on ACY Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	F [auth A], G [auth A]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A]
NA (Subject of Investigation/LOI) Query on NA Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]