8VZ3 | pdb_00008vz3

Structure of human PIN1 covalently derivatized with SuFEx compound

PDB DOI: https://doi.org/10.2210/pdb8VZ3/pdb

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

Deposited: 2024-02-09 Released: 2025-04-30
Deposition Author(s): Louie, G.V., Noel, J.P., Wang, W.-M., Kelly, J.W.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free:
0.221 (Depositor), 0.221 (DCC)
R-Value Work:
0.207 (Depositor), 0.207 (DCC)
R-Value Observed:
0.208 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Structure of human PIN1 covalently derivatized with SuFEx compound

Louie, G.V., Noel, J.P., Wang, W.-M., Kelly, J.W.

To be published.

Macromolecule Content

Total Structure Weight: 19.24 kDa
Atom Count: 1,385
Modeled Residue Count: 145
Deposited Residue Count: 167
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	167	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1AEL (Subject of Investigation/LOI) Query on A1AEL 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-(fluorosulfonyl)-5-({[(1S)-2-oxocyclopentyl]methyl}carbamoyl)benzoic acid C₁₄ H₁₄ F N O₆ S OHQBNPMKJCBHLK-QMMMGPOBSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], E [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.221 (Depositor), 0.221 (DCC)
R-Value Work: 0.207 (Depositor), 0.207 (DCC)
R-Value Observed: 0.208 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.881	α = 90
b = 68.881	β = 90
c = 79.663	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
iMOSFLM	data reduction
PHENIX	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-04-30

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-04-30
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.