MolNFT v1 · #24968 · protein

Structure of cyclophilin complexed with (D)ALA containing tetrapeptide

1VBS · Cyclophilin a: “Structure of cyclophilin complexed with (D)ALA containing tetrapeptide”. X-ray diffraction, 1 ligand (NIT), 1 pocket (best druggability 0.30). MolNFT v1 #24968 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 1VBS
Type: protein
Length: 168 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cyclophilin a; Tetrapeptide
UniProt: P05092
Ligands: NIT
Pockets: 1 · best druggability 0.30

Structure

x-ray diffraction · 2 distinct chains · 15% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cyclophilin a	protein	164	15% helix, 33% strand	P05092
B	Tetrapeptide	protein	4	0% helix, 25% strand	—

Ligands and binding sites

NIT · 4-nitroaniline · ligand · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	62	0.30	0.75	19	empty

Interfaces

1 interface between chains.

A–B · 262 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 covalent, 1 d-amino (covalent ligand, D-amino acid).

Compared structures

1VBS · Structure of cyclophilin complexed with (D)ALA containing tetrapeptide · 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 P05092
Elsewhere: RCSB PDB 1VBS · PDBe 1VBS · UniProt P05092

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