9IT1 | pdb_00009it1

Crystal structure of Pin1 using laue diffraction

PDB DOI: https://doi.org/10.2210/pdb9IT1/pdb

Classification: CELL CYCLE
Organism(s): Homo sapiens
Expression System: Escherichia
Mutation(s): No

Deposited: 2024-07-19 Released: 2024-08-21
Deposition Author(s): Sun, B., Qi, Q., Xiao, Q.J., Wang, Z.J.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.339 (Depositor), 0.338 (DCC)
R-Value Work:
0.318 (Depositor), 0.319 (DCC)
R-Value Observed:
0.320 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Crystal structure of Prolyl Isomerase NIMA-interacting 1 (Pin1) using laue diffraction

Sun, B., Qi, Q., Xiao, Q.J., Wang, Z.J.

To be published.

Macromolecule Content

Total Structure Weight: 18.49 kDa
Atom Count: 1,197
Modeled Residue Count: 145
Deposited Residue Count: 164
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	164	Homo sapiens	Mutation(s): 0 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
P3G Query on P3G 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]	3,6,9,12,15-PENTAOXAHEPTADECANE C₁₂ H₂₆ O₅ HYDWALOBQJFOMS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.339 (Depositor), 0.338 (DCC)
R-Value Work: 0.318 (Depositor), 0.319 (DCC)
R-Value Observed: 0.320 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.2	α = 90
b = 68.2	β = 90
c = 78.7	γ = 120

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-08-21

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32271248
National Natural Science Foundation of China (NSFC)	China	32200988

Revision History (Full details and data files)

Version 1.0: 2024-08-21
Type: Initial release

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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.