MolNFT v1 · #25033 · protein

Crystal structure of yeast cyclophilin a complexed with ACE-ala-ala- pro-ala-7-amino-4-methylcoumarin

1VDN: “Crystal structure of yeast cyclophilin a complexed with ACE-ala-ala- pro-ala-7-amino-4-methylcoumarin”. X-ray diffraction, 2 ligands (ACE, MCM). MolNFT v1 #25033 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1VDN
Type: protein
Length: 165 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cyclophilin a; (ACE)AAPA(MCM)
EC: 5.2.1.8
UniProt: P14832
Ligands: ACE, MCM

Structure

x-ray diffraction · 2 distinct chains · 14% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cyclophilin a (EC 5.2.1.8)	protein	161	14% helix, 32% strand	P14832
B	(ACE)AAPA(MCM)	protein	4	0% helix, 25% strand	—

Ligands and binding sites

ACE · Acetyl group · ligand · chains A, B
MCM · 7-amino-4-methyl-chromen-2-one · ligand · chains A, B

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

Interfaces

1 interface between chains.

A–B · 245 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

1VDN · Crystal Structure Of Yeast Cyclophilin A Complexed With… · the same entry in another collection · chain A against A, TM-score 1.00
P14832 · AlphaFold monomer V2.0 prediction for peptidyl-prolyl cis-trans isomerase (P14832) · a predicted model of the same protein · 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 P14832
Elsewhere: RCSB PDB 1VDN · PDBe 1VDN · UniProt P14832

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