4TNS | pdb_00004tns

Structure of Pin1 PPIase domain bound with all-trans retinoic acid

PDB DOI: https://doi.org/10.2210/pdb4TNS/pdb

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

Deposited: 2014-06-04 Released: 2015-04-08
Deposition Author(s): Li, W.Z., Zhang, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.33 Å
R-Value Free:
0.187 (Depositor), 0.202 (DCC)
R-Value Work:
0.169 (Depositor)
R-Value Observed:
0.170 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Structure of Pin1 PPIase domain bound with all-trans retinoic acid

Li, W.Z., Zhang, Y.

To be published.

Macromolecule Content

Total Structure Weight: 33.57 kDa
Atom Count: 1,999
Modeled Residue Count: 227
Deposited Residue Count: 302
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1	A, B	151	Homo sapiens	Mutation(s): 2 Gene Names: PIN1 EC: 5.2.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for Q13526 (Homo sapiens) Explore Q13526 Go to UniProtKB: Q13526
PHAROS: Q13526 GTEx: ENSG00000127445
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q13526
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
REA Query on REA 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]	RETINOIC ACID C₂₀ H₂₈ O₂ SHGAZHPCJJPHSC-YCNIQYBTSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.33 Å
R-Value Free: 0.187 (Depositor), 0.202 (DCC)
R-Value Work: 0.169 (Depositor)
R-Value Observed: 0.170 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.806	α = 90
b = 36.294	β = 100.92
c = 51.703	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2015-04-08

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-04-08
Type: Initial release
Version 1.1: 2016-10-26
Changes: Non-polymer description
Version 1.2: 2023-09-27
Changes: Data collection, Database references, Derived calculations, 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.