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Crystal structure of human ribokinase in C2 spacegroup

Analyse Crystal structure of human ribokinase in C2 spacegroup in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5BYC
Type: protein
Length: 634 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: NA
Pockets: 4 · best druggability 0.69

Structure

x-ray diffraction · 2 distinct chains · 38% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ribokinase (EC 2.7.1.15)	protein	318	37% helix, 23% strand	Q9H477
B	Ribokinase (EC 2.7.1.15)	protein	316	38% helix, 23% strand	Q9H477

Ligands and binding sites

NA · Sodium ion · metal · 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	686	0.69	0.77	98	empty
2	524	0.65	0.76	65	empty
3	50	0.30	0.76	12	empty
4	56	0.29	0.75	16	empty

Interfaces

1 interface between chains.

A–B · 1249 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

Q9H477 · AlphaFold monomer V2.0 prediction for ribokinase (Q9H477) · a predicted model of the same protein · chain B against A, TM-score 0.98

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 Q9H477
Elsewhere: RCSB PDB 5BYC · PDBe 5BYC · UniProt Q9H477

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