4N1N | pdb_00004n1n

Structure of Cyclophilin A in complex with Benzamide.

PDB DOI: https://doi.org/10.2210/pdb4N1N/pdb

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

Deposited: 2013-10-04 Released: 2015-08-12
Deposition Author(s): Mcnae, I.W., Dornan, J., Walkinshaw, M.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.213 (Depositor), 0.216 (DCC)
R-Value Work:
0.166 (Depositor), 0.169 (DCC)
R-Value Observed:
0.169 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4N1N

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

Literature

Mapping the binding surface of Cyclophilin A.

Mcnae, I.W., Dornan, D., Patterson, A.F., Wear, M.A., Blackburn, E.A., Walkinshaw, M.D.

To be published.

Macromolecule Content

Total Structure Weight: 18.16 kDa
Atom Count: 1,459
Modeled Residue Count: 165
Deposited Residue Count: 165
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase A	A	165	Homo sapiens	Mutation(s): 0 Gene Names: PPIA, CYPA EC: 5.2.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for P62937 (Homo sapiens) Explore P62937 Go to UniProtKB: P62937
PHAROS: P62937 GTEx: ENSG00000196262
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62937
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UNU Query on UNU Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	BENZAMIDE C₇ H₇ N O KXDAEFPNCMNJSK-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.213 (Depositor), 0.216 (DCC)
R-Value Work: 0.166 (Depositor), 0.169 (DCC)
R-Value Observed: 0.169 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.91	α = 90
b = 53.61	β = 90
c = 87.62	γ = 90

Software Package:

Software Name	Purpose
DNA	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2015-08-12

Deposition Author(s):

Walkinshaw, M.D.

Revision History (Full details and data files)

Version 1.0: 2015-08-12
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.