8UC5 | pdb_00008uc5

Apo X-ray crystal structure of Cyclophilin D with a surface entropy reduction mutation (K175I)

PDB DOI: https://doi.org/10.2210/pdb8UC5/pdb

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

Deposited: 2023-09-25 Released: 2024-09-04
Deposition Author(s): Kreitler, D.F., Rangwala, A.M., Seeliger, M.A.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.43 Å
R-Value Free:
0.175 (Depositor), 0.176 (DCC)
R-Value Work:
0.144 (Depositor), 0.144 (DCC)
R-Value Observed:
0.145 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Apo X-ray crystal structure of Cyclophilin D with a surface entropy reduction mutation (K175I)

Kreitler, D.F., Seeliger, M.A., Rangwala, A.M.

To be published.

Macromolecule Content

Total Structure Weight: 54.61 kDa
Atom Count: 4,190
Modeled Residue Count: 495
Deposited Residue Count: 498
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase F, mitochondrial	A [auth X], B [auth A], C [auth B]	166	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain I [auth X] SDF format, chain H [auth X] SDF format, chain G [auth X] SDF format, chain F [auth X] SDF format, chain E [auth X] SDF format, chain D [auth X] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain I [auth X] MOL2 format, chain H [auth X] MOL2 format, chain G [auth X] MOL2 format, chain F [auth X] MOL2 format, chain E [auth X] MOL2 format, chain D [auth X] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain I [auth X] mmCIF format, chain H [auth X] mmCIF format, chain G [auth X] mmCIF format, chain F [auth X] mmCIF format, chain E [auth X] mmCIF format, chain D [auth X]	D [auth X] E [auth X] F [auth X] G [auth X] H [auth X] D [auth X], E [auth X], F [auth X], G [auth X], H [auth X], I [auth X], M [auth A], N [auth A], O [auth A], R [auth B], S [auth B]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain D [auth X] Focus chain E [auth X] Focus chain F [auth X] Focus chain G [auth X] Focus chain H [auth X] Focus chain I [auth X] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain R [auth B] Focus chain S [auth B] Interactions & Density Focus chain D [auth X] Focus chain E [auth X] Focus chain F [auth X] Focus chain G [auth X] Focus chain H [auth X] Focus chain I [auth X] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain R [auth B] Focus chain S [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain Q [auth A] SDF format, chain L [auth X] SDF format, chain K [auth X] MOL2 format, chain Q [auth A] MOL2 format, chain L [auth X] MOL2 format, chain K [auth X] mmCIF format, chain Q [auth A] mmCIF format, chain L [auth X] mmCIF format, chain K [auth X]	K [auth X], L [auth X], Q [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain K [auth X] Focus chain L [auth X] Focus chain Q [auth A] Interactions & Density Focus chain K [auth X] Focus chain L [auth X] Focus chain Q [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain P [auth A] SDF format, chain J [auth X] MOL2 format, chain P [auth A] MOL2 format, chain J [auth X] mmCIF format, chain P [auth A] mmCIF format, chain J [auth X]	J [auth X], P [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain J [auth X] Focus chain P [auth A] Interactions & Density Focus chain J [auth X] Focus chain P [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.43 Å
R-Value Free: 0.175 (Depositor), 0.176 (DCC)
R-Value Work: 0.144 (Depositor), 0.144 (DCC)
R-Value Observed: 0.145 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.667	α = 90
b = 56.643	β = 123.72
c = 101.172	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DIMPLE	phasing
XDS	data reduction
Aimless	data scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-09-04

Deposition Author(s):

Kreitler, D.F.

Rangwala, A.M.

Seeliger, M.A.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P30GM133893
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM119437
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	F30CA260771