MolNFT v1 · #142212 · protein

Ribokinase from leishmania donovani

5ZWY: “Ribokinase from leishmania donovani”. X-ray diffraction, 2 ligands (NA, CL), 3 pockets (best druggability 0.70). MolNFT v1 #142212 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5ZWY
Type: protein
Length: 632 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: NA, CL
Pockets: 3 · best druggability 0.70

Structure

x-ray diffraction · 2 distinct chains · 39% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ribokinase (EC 2.7.1.15)	protein	307	39% helix, 23% strand	E9BIX7
B	Ribokinase (EC 2.7.1.15)	protein	325	38% helix, 22% strand	E9BIX7

Ligands and binding sites

NA · Sodium ion · metal · 7 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	642	0.70	0.78	72	GOL, CL
2	727	0.69	0.76	74	GOL, CL
3	70	0.31	0.75	19	empty

Interfaces

1 interface between chains.

A–B · 1374 Å² buried · 23 hydrogen bonds · protein-protein

Compared structures

5ZWY · Ribokinase from Leishmania donovani · 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 5ZWY · PDBe 5ZWY · UniProt E9BIX7

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