MolNFT v1 · #142566 · protein

Ribokinase from leishmania donovani with ADP

6A8C: “Ribokinase from leishmania donovani with ADP”. X-ray diffraction, 3 ligands (ADP, NA, CL), 4 pockets (best druggability 0.70). MolNFT v1 #142566 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6A8C
Type: protein
Length: 654 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ribokinase
EC: 2.7.1.15
UniProt: E9BIX7
Ligands: ADP, NA, CL
Pockets: 4 · best druggability 0.70

Structure

x-ray diffraction · 1 distinct chain · 37% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Ribokinase (EC 2.7.1.15)	protein	327	37% helix, 23% strand	E9BIX7

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
NA · Sodium ion · metal · 9 copies · chains A, B
CL · Chloride ion · ion · 9 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

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	662	0.70	0.78	80	GOL, CL, ADP
2	613	0.68	0.77	67	GOL, ADP
3	54	0.26	0.74	14	NA
4	64	0.26	0.72	17	CL

Interfaces

1 interface between chains.

A–B · 1361 Å² buried · 23 hydrogen bonds · protein-protein

Compared structures

6A8C · Ribokinase from Leishmania donovani with ADP · 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 E9BIX7
Elsewhere: RCSB PDB 6A8C · PDBe 6A8C · UniProt E9BIX7

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