9JJS: Human Pin1 catalytic domain

Crystal Structure of human Pin1 catalytic domain in complex with a covalent inhibitor. Determined by X-ray diffraction at 1.52 Å resolution. Released 25 Mar 2026.

Method: X-ray diffraction
Resolution: 1.52 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,003
Mol. weight: 27.3 kDa
Ligands: A1D9T
Released: 25 Mar 2026

Explore 9JJS in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9JJS contains 10 α-helices and 14 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	55-62	8	1
β-strand	72	1	2
β-strand	75	1	2
α-helix	82-98	17
α-helix	103-110	8
α-helix	114-118	5
β-strand	121-125	5	1
α-helix	132-140	9
α-helix	142	1
β-strand	146	1	1
β-strand	150-152	3	1
β-strand	155-161	7	1

Chain B: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	55-62	8	3
β-strand	72	1	4
β-strand	75	1	4
α-helix	82-97	16
α-helix	103-110	8
α-helix	114-118	5
β-strand	121-125	5	3
α-helix	132-139	8
α-helix	142	1
β-strand	146	1	3
β-strand	150-152	3	3
β-strand	155-161	7	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1	A, B	protein	121	Homo sapiens	Q13526 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>9JJS_1 Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (chains A, B)
GPGKNGQGEPARVRCSHLLVKHSQSRRPSSWRQEQITRTQEEALELINGYIQKIKSGEED
FESLASQFSDCSSAKARGDLGAFSRGQMQKPFEDASFALRTGEMSGPVFTDSGIHIILRT
E

Ligands and cofactors

ID	Name	Formula	Copies
A1D9T	methyl (~{E})-4-[[(3~{R})-1,1-bis(oxidanylidene)thiolan-3-yl]amino]-4-oxidanyli…	C9 H13 N O5 S	2

Primary citation

Crystal Structure of human Pin1 catalytic domain in complex with a covalent inhibitor. Wang, X.Y., Tian, M.Z., Zhou, J. et al. To be published.

Other PDB entries of the same protein (UniProt Q13526 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7AZ2 1.08 Å, 14-3-3 sigma with Pin1 binding site pS72 and covalently bound LvD1014
7AZ1 1.15 Å, 14-3-3 sigma with Pin1 binding site pS72 and covalently bound LvD1013
3I6C 1.3 Å, Structure-Based Design of Novel PIN1 Inhibitors (II)
4TNS 1.33 Å, Structure of Pin1 PPIase domain bound with all-trans retinoic acid
1PIN 1.35 Å, PIN1 peptidyl-prolyl cis-trans isomerase from homo sapiens
3TC5 1.4 Å, Selective targeting of disease-relevant protein binding domains by O-phosphorylated…
7AXN 1.4 Å, 14-3-3 sigma in complex with Pin1 binding site pS72 and covalently bound TCF521-026
7BG3 1.4 Å, 14-3-3 sigma with Pin1 binding site pS72 and covalently bound PC2046
6VAJ 1.42 Å, Crystal Structure Analysis of human PIN1
9KFZ 1.43 Å, Crystal structure of the PIN1 and fragment 59 complex
2ITK 1.45 Å, human Pin1 bound to D-PEPTIDE
2ZQT 1.46 Å, Crystal structure of a mutant PIN1 PEPTIDYL-PROLYL CIS-TRANS ISOMERASE

Browse structure collections

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