9JYS | pdb_00009jys

Crystal structure of the PIN1 and fragment 5 complex.

• PDB DOI: https://doi.org/10.2210/pdb9JYS/pdb

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


• Deposited: 2024-10-12 Released: 2025-10-15 
• Deposition Author(s): Xiao, Q.J., Wu, T.T., Shu, H.L., Qin, W.M.
• Funding Organization(s): Not funded

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.237 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.211 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Model: experimental

Literature

Fragment-Based Compound Screening Based on PIN1 Crystals

Xiao, Q.J., Wu, T.T., Huang, L., Qin, W.M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 18.9 kDa 
• Atom Count: 1,338 
• Modeled Residue Count: 147 
• Deposited Residue Count: 163 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1	A	163	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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PE8	C [auth A]	3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL C16 H34 O9 GLZWNFNQMJAZGY-UHFFFAOYSA-N
A1ED1 (Subject of Investigation/LOI)	B [auth A]	4-(aminomethyl)-N,N-dimethyl-aniline C9 H14 N2 PDJZOFLRRJQYBF-UHFFFAOYSA-N
SO4	D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.237 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.211 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.171	α = 90
b = 69.171	β = 90
c = 79.475	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data scaling
HKL-3000	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-10-15 
Deposition Author(s): Xiao, Q.J., Wu, T.T., Shu, H.L., Qin, W.M.

---

Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-10-15
  Type: Initial release