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Crystal structure of human ribokinase

Analyse Crystal structure of human ribokinase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2FV7
Type: protein
Length: 616 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ribokinase
EC: 2.7.1.15
UniProt: Q9H477
Ligands: ADP, NA, MG, UNX
Pockets: 3 · best druggability 0.74

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Ribokinase (EC 2.7.1.15)	protein	308	39% helix, 23% strand	Q9H477

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
NA · Sodium ion · metal · 2 copies · chains A, B
MG · Magnesium ion · metal · 2 copies · chains A, B
UNX · Unknown atom or ion · ion · 12 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	896	0.74	0.78	103	UNX, MG, ADP
2	400	0.61	0.77	57	MG, ADP, UNX
3	71	0.32	0.75	20	UNX

Interfaces

1 interface between chains.

A–B · 630 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

2FV7 · Crystal structure of human ribokinase · the same entry in another collection · chain A against A, TM-score 1.00
Q9H477 · AlphaFold monomer V2.0 prediction for ribokinase (Q9H477) · a predicted model of the same protein · chain A against A, TM-score 0.99

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Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q9H477
Elsewhere: RCSB PDB 2FV7 · PDBe 2FV7 · UniProt Q9H477

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