3UI6 | pdb_00003ui6

0.89 A resolution crystal structure of human Parvulin 14 in complex with oxidized DTT

PDB DOI: https://doi.org/10.2210/pdb3UI6/pdb

Classification: ISOMERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2011-11-04 Released: 2012-11-07
Deposition Author(s): Mueller, J.W., Link, N.M., Matena, A., Hoppstock, L., Rueppel, A., Bayer, P., Blankenfeldt, W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 0.89 Å
R-Value Free:
0.116 (Depositor), 0.123 (DCC)
R-Value Work:
0.103 (Depositor), 0.113 (DCC)
R-Value Observed:
0.103 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

0.89 A resolution crystal structure of human Parvulin 14 in complex with oxidized DTT

Mueller, J.W., Link, N.M., Matena, A., Hoppstock, L., Rueppel, A., Bayer, P., Blankenfeldt, W.

To be published.

Macromolecule Content

Total Structure Weight: 11.84 kDa
Atom Count: 1,077
Modeled Residue Count: 101
Deposited Residue Count: 101
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase NIMA-interacting 4	A	101	Homo sapiens	Mutation(s): 0 Gene Names: PIN4, Q9Y237 EC: 5.2.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y237 (Homo sapiens) Explore Q9Y237 Go to UniProtKB: Q9Y237
PHAROS: Q9Y237 GTEx: ENSG00000102309
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9Y237
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
D1D Query on D1D 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]	(4S,5S)-1,2-DITHIANE-4,5-DIOL C₄ H₈ O₂ S₂ YPGMOWHXEQDBBV-QWWZWVQMSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A], I [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 0.89 Å
R-Value Free: 0.116 (Depositor), 0.123 (DCC)
R-Value Work: 0.103 (Depositor), 0.113 (DCC)
R-Value Observed: 0.103 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.24	α = 90
b = 47.02	β = 90
c = 51.85	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2012-11-07

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-11-07
Type: Initial release
Version 1.1: 2012-12-05
Changes: Structure summary
Version 1.2: 2018-01-31
Changes: Database references
Version 1.3: 2024-02-28
Changes: Data collection, Database references, Derived calculations