MolNFT v1 · #115967 · protein

The structure of vink

5CZC · Malonyl-CoA-[acyl-carrier-protein] transacylase: “The structure of vink”. X-ray diffraction, 1 ligand (CA), 6 pockets (best druggability 0.81). MolNFT v1 #115967 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5CZC
Type: protein
Length: 601 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Malonyl-CoA-[acyl-carrier-protein] transacylase
UniProt: Q76KY5
Ligands: CA
Pockets: 6 · best druggability 0.81

Structure

x-ray diffraction · 2 distinct chains · 51% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Malonyl-CoA-[acyl-carrier-protein] transacylase	protein	300	50% helix, 19% strand	Q76KY5
B	Malonyl-CoA-[acyl-carrier-protein] transacylase	protein	301	51% helix, 19% strand	Q76KY5

Ligands and binding sites

CA · Calcium ion · metal · 2 copies · chains A, B
GOL · Glycerol · additive · 2 copies · chains A, B

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

Pockets

6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	116	0.81	0.99	28	GOL
2	125	0.79	0.97	23	GOL
3	840	0.75	0.79	84	empty
4	132	0.56	0.82	27	empty
5	66	0.30	0.74	20	empty

Interfaces

1 interface between chains.

A–B · 323 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

5CZC · The structure of VinK · 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 Q76KY5
Elsewhere: RCSB PDB 5CZC · PDBe 5CZC · UniProt Q76KY5

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