5CCN

Human Cyclophilin D Complexed with Inhibitor

PDB DOI: https://doi.org/10.2210/pdb5CCN/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: 1.80 Å
R-Value Free: 0.207
R-Value Work: 0.179
R-Value Observed: 0.180

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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: 18.52 kDa
Atom Count: 1,421
Modelled Residue Count: 164
Deposited Residue Count: 164
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase F, mitochondrial	A	164	Homo sapiens	Mutation(s): 1 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P30405
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
4ZZ Query on 4ZZ Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	ethyl N-{[3-(3-aminopyridin-4-yl)benzyl]carbamoyl}glycinate C₁₇ H₂₀ N₄ O₃ BMVIHQIQLWPWDF-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
PG4 Query on PG4 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]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
PGE Query on PGE 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]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
K Query on K 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]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]