9KFZ: PIN1 and fragment 59 complex

Crystal structure of the PIN1 and fragment 59 complex. Determined by X-ray diffraction at 1.43 Å resolution. Released 12 Nov 2025.

Method: X-ray diffraction
Resolution: 1.43 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,393
Mol. weight: 19.3 kDa
Ligands: PE8, A1EFO
Released: 12 Nov 2025

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

Secondary structure: helices and β-sheets

9KFZ contains 6 α-helices and 10 β-strands across 1 chain. 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: 6 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	11-15	5	1
β-strand	22-26	5	1
β-strand	32-33	2	1
α-helix	36-38	3
β-strand	54-62	9	2
β-strand	72	1	3
β-strand	75	1	3
α-helix	82-98	17
α-helix	103-110	8
α-helix	114-118	5
β-strand	121-126	6	2
α-helix	132-140	9
α-helix	142	1
β-strand	146	1	2
β-strand	150-151	2	2
β-strand	156-161	6	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1	A	protein	163	Homo sapiens	Q13526 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9KFZ_1 Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (chains A)
MADEEKLPPGWEKAMSRSSGRVYYFNHITNASQWERPSGNSSSGGKNGQGEPARVRCSHL
LVKHSQSRRPSSWRQEKITRTKEEALELINGYIQKIKSGEEDFESLASQFSDCSSAKARG
DLGAFSRGQMQKPFEDASFALRTGEMSGPVFTDSGIHIILRTE

Ligands and cofactors

ID	Name	Formula	Copies
PE8	3,6,9,12,15,18,21-heptaoxatricosane-1,23-diol	C16 H34 O9	1
A1EFO	6-methylpyridine-2-carboxylic acid	C7 H7 N O2	4

Water and common crystallization additives (SO4) are not listed.

Primary citation

Fragment-Based Compound Screening Based on PIN1 Crystals. Xiao, Q.J., Wu, T.T., Shu, H.L. 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
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
2F21 1.5 Å, human Pin1 Fip mutant

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