6GJY: Cyclophilin A

Cyclophilin A complexed with tri-vector ligand 5. Determined by X-ray diffraction at 1.29 Å resolution. Released 7 Nov 2018.

Method: X-ray diffraction
Resolution: 1.29 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,662
Mol. weight: 18.33 kDa
Ligands: F1Z
Released: 7 Nov 2018

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

Secondary structure: helices and β-sheets

6GJY contains 4 α-helices and 13 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: 4 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	3
β-strand	5-12	8	1
β-strand	15-24	10	1
α-helix	30-41	12
β-strand	52	1	1
β-strand	55-57	3	1
β-strand	61-64	4	1
β-strand	77-78	2	2
β-strand	80	1	2
β-strand	83	1	3
β-strand	97-100	4	1
β-strand	108	1	3
β-strand	112-115	4	1
α-helix	120-122	3
β-strand	128-134	7	1
α-helix	136-143	8
β-strand	156-164	9	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Peptidyl-prolyl cis-trans isomerase A	A	protein	165	Homo sapiens	P62937 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6GJY_1 Peptidyl-prolyl cis-trans isomerase A (chains A)
MVNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGF
MCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTE
WLDGKHVVFGKVKEGMNIVEAMERFGSRNGKTSKKITIADCGQLE

Ligands and cofactors

ID	Name	Formula	Copies
F1Z	ethyl 2-[[(4-aminophenyl)methyl-prop-2-ynyl-carbamoyl]amino]ethanoate	C15 H19 N3 O3	1

Primary citation

A computationally designed binding mode flip leads to a novel class of potent tri-vector cyclophilin inhibitors. De Simone, A., Georgiou, C., Ioannidis, H. et al. Chem Sci (2019) 10:542-547. DOI 10.1039/c8sc03831g · PubMed

Other PDB entries of the same protein (UniProt P62937 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9E3S 1.08 Å, Tricomplex of RMC-9945, KRAS G12N, and CypA
9BG4 1.14 Å, Tri-complex of Compound-2, KRAS G12V, and CypA
4N1M 1.15 Å, Structure of Cyclophilin A in complex with GlyPro.
5F66 1.15 Å, High-resolution isotropic multiconformer synchrotron model of CypA at 273 K
9GHY 1.15 Å, Cyclophilin A in complex with Sanglifehrin A analogue (2R,3S,7S,10S,E)-10-(3-aminopropyl)…
6GJL 1.16 Å, Cyclophilin A complexed with tri-vector ligand 10.
6GS6 1.16 Å, Cyclophilin A single mutant D66A in complex with an inhibitor.
2X25 1.2 Å, Free acetyl-CypA orthorhombic form
4YUO 1.2 Å, High-resolution multiconformer synchrotron model of CypA at 273 K
7UXM 1.2 Å, Structure of PPIA in complex with FP29092, a Helicon Polypeptide
8TBG 1.2 Å, Tricomplex of RMC-7977, HRAS WT, and CypA
9BFV 1.2 Å, Tri-complex of Compound-23, KRAS G12C, and CypA

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