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Crystal structure of ribose-5-isomerase a

Analyse Crystal structure of ribose-5-isomerase a in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3KWM
Type: protein
Length: 871 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ribose-5-phosphate isomerase a
EC: 5.3.1.6
UniProt: Q5NFM5
Ligands: 3GR, NA, PO4
Pockets: 12 · best druggability 0.75

Structure

x-ray diffraction · 2 distinct chains · 34% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, D	Ribose-5-phosphate isomerase a (EC 5.3.1.6)	protein	218	33% helix, 29% strand	Q5NFM5
B	Ribose-5-phosphate isomerase a (EC 5.3.1.6)	protein	217	35% helix, 29% strand	Q5NFM5

Ligands and binding sites

3GR · D-Glyceraldehyde · ligand · chains D
NA · Sodium ion · metal · 2 copies · chains A, D, B, C
PO4 · Phosphate ion · ion · 3 copies · chains A, B, D
PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains C

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

Pockets

12 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	576	0.75	0.82	77	PO4
2	104	0.58	0.86	34	NA
3	99	0.52	0.83	26	NA
4	82	0.48	0.82	22	empty
5	158	0.44	0.75	20	empty

Interfaces

3 interfaces between chains.

A–D · 1288 Å² buried · 16 hydrogen bonds · protein-protein
B–C · 1282 Å² buried · 10 hydrogen bonds · protein-protein
A–C · 829 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

3KWM · Crystal structure of ribose-5-isomerase A · the same entry in another collection · chain A against A, TM-score 1.00
Q5NFM5 · AlphaFold monomer V2.0 prediction for ribose-5-phosphate isomerase a (Q5NFM5) · 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 Q5NFM5
Elsewhere: RCSB PDB 3KWM · PDBe 3KWM · UniProt Q5NFM5

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