MolNFT v1 · #144963 · protein

Mycobacterium tuberculosis adenosine kinase bound to (2R,3S,4R,5R)-2- (hydroxymethyl)-5-(6-(4-phenylpiperazin-1-yl)-9H-purin-9-yl) tetrahydrofuran-3,4-diol

6C9V: “Mycobacterium tuberculosis adenosine kinase bound to (2R,3S,4R,5R)-2…”. X-ray diffraction, 3 ligands (ERS, NA, SO4), 2 pockets (best druggability 0.77). MolNFT v1 #144963 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6C9V
Type: protein
Length: 630 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Adenosine kinase
EC: 2.7.1.20
UniProt: A5U4N0
Ligands: ERS, NA, SO4
Pockets: 2 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 43% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Adenosine kinase (EC 2.7.1.20)	protein	315	43% helix, 23% strand	A5U4N0

Ligands and binding sites

ERS · (2R,3S,4R,5R)-2-(hydroxymethyl)-5-[6-(4-phenylpiperazin-1-yl)-9H-purin-9-yl]tetrahydrofuran-3, 4-diol · ligand · 2 copies · chains A, B
NA · Sodium ion · metal · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 2 copies · chains A, B
GOL · Glycerol · additive · chains A, B

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

Pockets

2 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	736	0.77	0.81	63	ERS, SO4
2	747	0.76	0.81	60	ERS, SO4

Interfaces

1 interface between chains.

A–B · 1179 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

6C9V · Mycobacterium tuberculosis adenosine kinase bound to… · the same entry in another collection · chain A against A, TM-score 1.00
A5U4N0 · AlphaFold monomer V2.0 prediction for adenosine kinase (A5U4N0) · a predicted model of the same protein · chain B against A, TM-score 0.99

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 A5U4N0
Elsewhere: RCSB PDB 6C9V · PDBe 6C9V · UniProt A5U4N0

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