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Structure of arabidopsis thaliana ribokinase complexed with ribose and ATP

Analyse Structure of arabidopsis thaliana ribokinase complexed with ribose and ATP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6ILS
Type: protein
Length: 625 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ribokinase
EC: 2.7.1.15
UniProt: A1A6H3
Ligands: ATP, RIB, NA
Pockets: 5 · best druggability 0.70

Structure

x-ray diffraction · 2 distinct chains · 37% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ribokinase (EC 2.7.1.15)	protein	312	38% helix, 25% strand	A1A6H3
B	Ribokinase (EC 2.7.1.15)	protein	313	36% helix, 25% strand	A1A6H3

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
RIB · alpha-D-ribofuranose · ligand · chains B
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

5 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	599	0.70	0.79	65	ATP, RIB
2	526	0.64	0.76	59	ATP
3	128	0.42	0.75	24	empty
4	50	0.37	0.81	14	empty
5	89	0.34	0.74	23	empty

Interfaces

1 interface between chains.

A–B · 1342 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

6ILS · Structure of Arabidopsis thaliana Ribokinase complexed with Ribose and ATP · the same entry in another collection · chain A against A, TM-score 1.00
A1A6H3 · AlphaFold monomer V2.0 prediction for ribokinase (A1A6H3) · a predicted model of the same protein · chain B against A, TM-score 0.99

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 A1A6H3
Elsewhere: RCSB PDB 6ILS · PDBe 6ILS · UniProt A1A6H3

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