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Structural study of clostridium thermocellum ribose-5-phosphate isomerase B and ribose-5-phosphate

Analyse Structural study of clostridium thermocellum ribose-5-phosphate isomerase B and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3HEE
Type: protein
Length: 296 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ribose-5-phosphate isomerase
EC: 5.3.1.6
UniProt: A3DIL8
Ligands: R5P
Pockets: 3 · best druggability 0.57

Structure

x-ray diffraction · 1 distinct chain · 51% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Ribose-5-phosphate isomerase (EC 5.3.1.6)	protein	148	51% helix, 16% strand	A3DIL8

Ligands and binding sites

R5P · Ribose-5-phosphate · ligand · 2 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, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	55	0.57	0.91	17	R5P
2	56	0.56	0.90	17	R5P
3	53	0.53	0.89	17	empty

Interfaces

1 interface between chains.

A–B · 2052 Å² buried · 25 hydrogen bonds · protein-protein

Compared structures

3HEE · Structural study of Clostridium thermocellum Ribose-5-Phosphate Isomerase B and… · the same entry in another collection · chain A against A, TM-score 1.00

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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 A3DIL8
Elsewhere: RCSB PDB 3HEE · PDBe 3HEE · UniProt A3DIL8

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