Research workbench

Ribokinase from T.sp mutant A92G

Analyse Ribokinase from T.sp mutant A92G in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 8CQX
Type: protein
Length: 1,200 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.27
Source: Thermus sp.
Molecule: Ribokinase
UniProt: A0A0B0SD75
Ligands: ADP, MG
Pockets: 10 · best druggability 0.72

Structure

x-ray diffraction · resolution 2.27 · 1 distinct chain · 38% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Ribokinase	protein	300	38% helix, 24% strand	A0A0B0SD75

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
MG · Magnesium ion · metal · 3 copies · chains A, B, C

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

Pockets

10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	407	0.72	0.83	51	ADP
2	686	0.68	0.76	80	ADP
3	212	0.63	0.83	37	empty
4	420	0.62	0.77	67	ADP
5	184	0.56	0.80	26	ADP

Interfaces

3 interfaces between chains.

A–D · 1639 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 712 Å² buried · 4 hydrogen bonds · protein-protein
B–C · 283 Å² buried · 3 hydrogen bonds · protein-protein

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 A0A0B0SD75
Elsewhere: RCSB PDB 8CQX · PDBe 8CQX · UniProt A0A0B0SD75

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.