1E8K

Cyclophilin 3 Complexed With Dipeptide Ala-Pro

PDB DOI: https://doi.org/10.2210/pdb1E8K/pdb

Classification: ISOMERASE
Organism(s): Caenorhabditis elegans
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2000-09-25 Released: 2001-09-20
Deposition Author(s): Wu, S.Y., Dornan, J., Kontopidis, G., Taylor, P., Walkinshaw, M.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.251
R-Value Observed: 0.183

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

The First Direct Determination of a Ligand Binding Constant in Protein Crystals

Wu Sy, S.Y., Dornan, J., Kontopidis, G., Taylor, P., Walkinshaw, M.D.

(2001) Angew Chem Int Ed Engl 40: 582

PubMed: 11180378 Search on PubMed
Primary Citation of Related Structures:
1E8K

Organizational Affiliation

Structural Biochemistry Group Institute of Cell and Molecular Biology The University of Edinburgh Michael Swann Building, King's Buildings Mayfield Road, Edinburgh, EH9 3JR (UK).

Macromolecule Content

Total Structure Weight: 18.78 kDa
Atom Count: 1,546
Modelled Residue Count: 173
Deposited Residue Count: 173
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 3	A	173	Caenorhabditis elegans	Mutation(s): 0 EC: 5.2.1.8
UniProt
Find proteins for P52011 (Caenorhabditis elegans) Explore P52011 Go to UniProtKB: P52011
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P52011
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PRO Query on PRO 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]	PROLINE C₅ H₉ N O₂ ONIBWKKTOPOVIA-BYPYZUCNSA-N		Interactions Focus chain C [auth A]
ALA Query on ALA 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]	ALANINE C₃ H₇ N O₂ QNAYBMKLOCPYGJ-REOHCLBHSA-N		Interactions Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.251
R-Value Observed: 0.183
Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.035	α = 90
b = 61.035	β = 90
c = 122.66	γ = 90

Software Package:

Software Name	Purpose
SHELXL-97	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2001-09-20

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2001-09-20
Type: Initial release
Version 1.1: 2013-07-17
Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Other, Source and taxonomy, Structure summary, Version format compliance
Version 1.2: 2013-07-24
Changes: Derived calculations, Other
Version 1.3: 2018-06-20
Changes: Advisory, Data collection, Derived calculations
Version 1.4: 2019-05-22
Changes: Data collection, Refinement description
Version 1.5: 2023-12-13
Changes: Data collection, Database references, Refinement description