5CCS | pdb_00005ccs

Human Cyclophilin D Complexed with Inhibitor

PDB DOI: https://doi.org/10.2210/pdb5CCS/pdb

Classification: ISOMERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2015-07-02 Released: 2016-07-20
Deposition Author(s): Gibson, R.P., Shore, E., Kershaw, N., Awais, M., Javed, A., Latawiec, D., Pandalaneni, S., Wen, L., Berry, N., O'Neill, P., Sutton, R., Lian, L.Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.196 (Depositor), 0.212 (DCC)
R-Value Work:
0.160 (Depositor), 0.172 (DCC)
R-Value Observed:
0.162 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Human Cyclophilin D Complexed with Inhibitor

Gibson, R.P., Shore, E., Kershaw, N., Awais, M., Javed, A., Latawiec, D., Pandalaneni, S., Wen, L., Berry, N., O'Neill, P., Sutton, R., Lian, L.Y.

To be published.

Macromolecule Content

Total Structure Weight: 18.13 kDa
Atom Count: 1,375
Modeled Residue Count: 164
Deposited Residue Count: 165
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase F, mitochondrial	A [auth X]	165	Homo sapiens	Mutation(s): 2 Gene Names: PPIF, CYP3 EC: 5.2.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for P30405 (Homo sapiens) Explore P30405 Go to UniProtKB: P30405
PHAROS: P30405 GTEx: ENSG00000108179
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P30405
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
C4Y Query on C4Y Download:Ideal Coordinates CCD File SDF format, chain B [auth X] MOL2 format, chain B [auth X] mmCIF format, chain B [auth X]	B [auth X]	1-(4-aminobenzyl)-3-{2-oxo-2-[(2R)-2-phenylpyrrolidin-1-yl]ethyl}urea C₂₀ H₂₄ N₄ O₂ DBVKUBKWQMJAPI-GOSISDBHSA-N		Interactions Focus chain B [auth X] Interactions & Density Focus chain B [auth X]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.196 (Depositor), 0.212 (DCC)
R-Value Work: 0.160 (Depositor), 0.172 (DCC)
R-Value Observed: 0.162 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.27	α = 90
b = 58.7	β = 90
c = 77.03	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2016-07-20

Deposition Author(s):

Pandalaneni, S.

Revision History (Full details and data files)

Version 1.0: 2016-07-20
Type: Initial release
Version 1.1: 2024-01-10
Changes: Data collection, Database references, Refinement description

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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.