MolNFT v1 · #144959 · protein

Mycobacterium tuberculosis adenosine kinase bound to (2R,3S,4R,5R)-2- (hydroxymethyl)-5-(6-(thiophen-3-yl)-9H-purin-9-YL)TETRAHYDROFURAN-3, 4-diol

6C9R: “Mycobacterium tuberculosis adenosine kinase bound to (2R,3S,4R,5R)-2…”. X-ray diffraction, 2 ligands (ERJ, NA), 4 pockets (best druggability 0.78). MolNFT v1 #144959 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6C9R
Type: protein
Length: 674 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: ERJ, NA
Pockets: 4 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 45% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Adenosine kinase (EC 2.7.1.20)	protein	337	45% helix, 22% strand	A5U4N0

Ligands and binding sites

ERJ · 9-beta-D-ribofuranosyl-6-(thiophen-3-yl)-9H-purine · ligand · 4 copies · chains A, B
NA · Sodium ion · metal · 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

4 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	977	0.78	0.80	81	ERJ
2	901	0.77	0.80	74	ERJ
3	51	0.33	0.78	16	empty
4	50	0.27	0.75	17	empty

Interfaces

1 interface between chains.

A–B · 1487 Å² buried · 18 hydrogen bonds · protein-protein

Compared structures

6C9R · 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 0.94

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 6C9R · PDBe 6C9R · UniProt A5U4N0

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