4RUH | pdb_00004ruh

Crystal structure of Human Carnosinase-2 (CN2) in complex with inhibitor, Bestatin at 2.25 A

PDB DOI: https://doi.org/10.2210/pdb4RUH/pdb

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

Deposited: 2014-11-19 Released: 2015-11-25
Deposition Author(s): pandya, V., Kaushik, A., Singh, A.K., Singh, R.P., Kumaran, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free:
0.282 (Depositor), 0.279 (DCC)
R-Value Work:
0.219 (Depositor), 0.219 (DCC)
R-Value Observed:
0.222 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4RUH

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of Human Carnosinase-2 (CN2) in complex with inhibitor, Bestatin at 2.25 A

pandya, V., Kaushik, A., Singh, A.K., Singh, R.P., Kumaran, S.

To be published.

Macromolecule Content

Total Structure Weight: 106.91 kDa
Atom Count: 7,304
Modeled Residue Count: 911
Deposited Residue Count: 950
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytosolic non-specific dipeptidase	A, B	475	Homo sapiens	Mutation(s): 0 Gene Names: CN2, CNDP dipeptidase 2 (metallopeptidase M20 family) [ Homo sapiens (human), CNDP2, CPGL, PEPA EC: 3.4.13.18
UniProt & NIH Common Fund Data Resources
Find proteins for Q96KP4 (Homo sapiens) Explore Q96KP4 Go to UniProtKB: Q96KP4
PHAROS: Q96KP4 GTEx: ENSG00000133313
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q96KP4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BES Query on BES Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain F [auth B]	C [auth A], F [auth B]	2-(3-AMINO-2-HYDROXY-4-PHENYL-BUTYRYLAMINO)-4-METHYL-PENTANOIC ACID C₁₆ H₂₄ N₂ O₄ VGGGPCQERPFHOB-RDBSUJKOSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B]	I [auth B], J [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain I [auth B] Focus chain J [auth B]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain H [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B]	D [auth A], E [auth A], G [auth B], H [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.282 (Depositor), 0.279 (DCC)
R-Value Work: 0.219 (Depositor), 0.219 (DCC)
R-Value Observed: 0.222 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.09	α = 90
b = 100.07	β = 90
c = 105.83	γ = 90

Software Package:

Software Name	Purpose
MxCuBE	data collection
PHASES	phasing
PHENIX	refinement
iMOSFLM	data reduction
SCALA	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2015-11-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-11-25
Type: Initial release
Version 1.1: 2024-02-28
Changes: Data collection, Database references, Derived calculations

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.