MolNFT v1 · #25215 · protein

Crystal structure of dephospho-CoA kinase

1VIY: “Crystal structure of dephospho-CoA kinase”. X-ray diffraction, 1 ligand (SO4), 6 pockets (best druggability 0.80). MolNFT v1 #25215 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1VIY
Type: protein
Length: 624 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dephospho-CoA kinase
EC: 2.7.1.24
UniProt: P0A6I9
Ligands: SO4
Pockets: 6 · best druggability 0.80

Structure

x-ray diffraction · 1 distinct chain · 56% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Dephospho-CoA kinase (EC 2.7.1.24)	protein	208	56% helix, 13% strand	P0A6I9

Ligands and binding sites

SO4 · Sulfate ion · ion · 5 copies · chains A, B, C

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

Pockets

6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1198	0.80	0.81	143	empty
2	493	0.74	0.82	62	empty
3	260	0.55	0.76	27	empty
4	57	0.38	0.80	15	empty
5	81	0.36	0.76	15	empty

Interfaces

3 interfaces between chains.

A–C · 1095 Å² buried · 12 hydrogen bonds · protein-protein
B–C · 902 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 846 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

1VIY · Crystal structure of dephospho-CoA kinase · the same entry in another collection · chain A against A, TM-score 1.00
P0A6I9 · AlphaFold monomer V2.0 prediction for dephospho-CoA kinase (P0A6I9) · a predicted model of the same protein · chain B against A, TM-score 0.95

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 P0A6I9
Elsewhere: RCSB PDB 1VIY · PDBe 1VIY · UniProt P0A6I9

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