MolNFT v1 · #25176 · protein

Crystal structure of dephospho-CoA kinase with BIS(ADENOSINE)-5'- triphosphate

1VHT: “Crystal structure of dephospho-CoA kinase with BIS(ADENOSINE)-5'- triphosphate”. X-ray diffraction, 1 ligand (BA3), 7 pockets (best druggability 0.71). MolNFT v1 #25176 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1VHT
Type: protein
Length: 605 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: BA3
Pockets: 7 · best druggability 0.71

Structure

x-ray diffraction · 2 distinct chains · 53% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Dephospho-CoA kinase (EC 2.7.1.24)	protein	208	55% helix, 13% strand	P0A6I9
C	Dephospho-CoA kinase (EC 2.7.1.24)	protein	189	51% helix, 13% strand	P0A6I9

Ligands and binding sites

BA3 · Bis(adenosine)-5'-triphosphate · ligand · 3 copies · chains A, B, C
ACT · Acetate ion · additive · 2 copies · chains A, B

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

Pockets

7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	843	0.71	0.76	64	empty
2	399	0.61	0.76	36	ACT
3	139	0.45	0.76	19	ACT
4	112	0.42	0.76	19	empty
5	123	0.39	0.74	17	empty

Interfaces

1 interface between chains.

B–C · 307 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

1VHT · Crystal structure of dephospho-coA kinase with bis(adenosine)-5'-triphosphate · 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 0.92

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 1VHT · PDBe 1VHT · UniProt P0A6I9

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