Research workbench

Ribose 5-phosphate isomerase from plasmodium falciparum

Analyse Ribose 5-phosphate isomerase from plasmodium falciparum in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2F8M
Type: protein
Length: 472 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: Q8I3W2
Ligands: PO4
Pockets: 5 · best druggability 0.47

Structure

x-ray diffraction · 2 distinct chains · 29% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ribose 5-phosphate isomerase (EC 5.3.1.6)	protein	237	30% helix, 26% strand	Q8I3W2
B	Ribose 5-phosphate isomerase (EC 5.3.1.6)	protein	235	29% helix, 26% strand	Q8I3W2

Ligands and binding sites

PO4 · Phosphate ion · ion · 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, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	200	0.47	0.74	22	empty
2	192	0.47	0.75	21	empty
3	59	0.38	0.80	18	PO4
4	60	0.37	0.80	21	PO4
5	57	0.27	0.74	17	empty

Interfaces

1 interface between chains.

A–B · 1397 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

2F8M · Ribose 5-phosphate isomerase from Plasmodium falciparum · the same entry in another collection · chain A against A, TM-score 1.00
Q8I3W2 · AlphaFold monomer V2.0 prediction for ribose-5-phosphate isomerase (Q8I3W2) · 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 Q8I3W2
Elsewhere: RCSB PDB 2F8M · PDBe 2F8M · UniProt Q8I3W2

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