MolNFT v1 · #73819 · protein

Crystal structure of cyclophilin a in complex with voclosporin Z- ISA247

3ODL: “Crystal structure of cyclophilin a in complex with voclosporin Z- ISA247”. X-ray diffraction, 17 pockets (best druggability 0.74). MolNFT v1 #73819 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3ODL
Type: protein
Length: 1,760 residues
Chains: 20
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cyclophilin a; Voclosporin
EC: 5.2.1.8
UniProt: A8K220
Pockets: 17 · best druggability 0.74

Structure

x-ray diffraction · 2 distinct chains · 13% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E, G, I, K, M, O, Q, S	Cyclophilin a (EC 5.2.1.8)	protein	165	14% helix, 32% strand	A8K220
B, D, F, H, J, L, N, P, R, T	Voclosporin	protein	11	0% helix, 9% strand	—

Pockets

17 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1033	0.74	0.77	113	empty
2	1031	0.73	0.76	122	empty
3	709	0.72	0.78	72	empty
4	886	0.70	0.76	107	empty
5	534	0.67	0.78	51	empty

Interfaces

55 interfaces between chains.

G–H · 537 Å² buried · 8 hydrogen bonds · protein-protein
K–L · 533 Å² buried · 7 hydrogen bonds · protein-protein
Q–R · 531 Å² buried · 7 hydrogen bonds · protein-protein
I–J · 500 Å² buried · 7 hydrogen bonds · protein-protein
O–P · 498 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 80 modified, 10 d-amino (nonstandard, methylation, D-amino acid).

Compared structures

3ODL · Crystal structure of cyclophilin A in complex with Voclosporin Z-ISA247 · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt A8K220
Elsewhere: RCSB PDB 3ODL · PDBe 3ODL · UniProt A8K220

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