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Ribokinase from leishmania donovani with amppcp

Analyse Ribokinase from leishmania donovani with amppcp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6A8B
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: ACP, NA, CL
Pockets: 3 · best druggability 0.67

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Ribokinase (EC 2.7.1.15)	protein	327	38% helix, 23% strand	E9BIX7

Ligands and binding sites

ACP · Phosphomethylphosphonic acid adenylate ester · ligand · 2 copies · chains A, B
NA · Sodium ion · metal · 6 copies · chains A, B
CL · Chloride ion · ion · 7 copies · chains A, B
GOL · Glycerol · additive · 3 copies · chains A, B

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

Pockets

3 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	558	0.67	0.77	68	ACP, CL
2	586	0.66	0.77	73	ACP, GOL, CL
3	56	0.28	0.75	16	empty

Interfaces

1 interface between chains.

A–B · 1372 Å² buried · 23 hydrogen bonds · protein-protein

Compared structures

6A8B · Ribokinase from Leishmania donovani with AMPPCP · 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 6A8B · PDBe 6A8B · UniProt E9BIX7

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