6VAJ: Crystal Structure Analysis of human PIN1

Crystal Structure Analysis of human PIN1. Determined by X-ray diffraction at 1.42 Å resolution. Released 30 Dec 2020.

Method: X-ray diffraction
Resolution: 1.42 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,384
Mol. weight: 20.51 kDa
Ligands: QT7
Released: 30 Dec 2020

Explore 6VAJ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6VAJ contains 6 α-helices and 8 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, 8 β-strands

Element	Residues	Length	Sheet
α-helix	7-8	2
β-strand	11-15	5	1
β-strand	22-26	5	1
β-strand	32-33	2	1
β-strand	55-62	8	2
α-helix	82-98	17
α-helix	103-110	8
α-helix	114-118	5
β-strand	121-125	5	2
α-helix	132-140	9
α-helix	142	1
β-strand	146	1	2
β-strand	150-152	3	2
β-strand	155-161	7	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1	A	protein	178	Homo sapiens	Q13526 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6VAJ_1 Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (chains A)
GSHMARGCRNSARGKMADEEKLPPGWEKRMSRSSGRVYYFNHITNASQWERPSGNSSSGG
KNGQGEPARVRCSHLLVKHSQSRRPSSWRQEQITRTQEEALELINGYIQKIKSGEEDFES
LASQFSDCSSAKARGDLGAFSRGQMQKPFEDASFALRTGEMSGPVFTDSGIHIILRTE

Ligands and cofactors

ID	Name	Formula	Copies
QT7	2-chloro-N-(2,2-dimethylpropyl)-N-[(3R)-1,1-dioxo-1lambda~6~-thiolan-3-yl]aceta…	C11 H20 Cl N O3 S	1

Water and common crystallization additives (SO4, PG4) are not listed.

Primary citation

Sulfopin is a covalent inhibitor of Pin1 that blocks Myc-driven tumors in vivo. Dubiella, C., Pinch, B.J., Koikawa, K. et al. Nat Chem Biol (2021) 17:954-963. DOI 10.1038/s41589-021-00786-7 · PubMed

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
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
2F21 1.5 Å, human Pin1 Fip mutant

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