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Complex Structure of D-ribose Pyranase Sa240 with D-ribose

Analyse Complex Structure of D-ribose Pyranase Sa240 with D-ribose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3P13
Type: protein
Length: 518 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.35
Source: Staphylococcus aureus
Molecule: D-ribose pyranase
EC: 5.5.1.-
UniProt: Q2G1A5
Ligands: RIP
Pockets: 4 · best druggability 0.67

Structure

x-ray diffraction · resolution 2.35 · 2 distinct chains · 32% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	D-ribose pyranase (EC 5.5.1.-)	protein	130	32% helix, 25% strand	Q2G1A5
B, D	D-ribose pyranase (EC 5.5.1.-)	protein	129	33% helix, 26% strand	Q2G1A5

Ligands and binding sites

RIP · beta-D-ribopyranose · sugar · 4 copies · chains A, B, C, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	710	0.67	0.75	51	RIP
2	113	0.37	0.74	28	empty
3	102	0.34	0.73	16	empty
4	53	0.25	0.73	15	empty

Interfaces

5 interfaces between chains.

A–D · 942 Å² buried · 10 hydrogen bonds · protein-protein
B–C · 934 Å² buried · 10 hydrogen bonds · protein-protein
A–C · 338 Å² buried · 0 hydrogen bonds · protein-protein
C–D · 35 Å² buried · 0 hydrogen bonds · protein-protein
A–B · 34 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

3P13 · Complex structure of D-ribose pyranase SA240 with D-ribose · the same entry in another collection · chain A against A, TM-score 1.00
Q2G1A5 · AlphaFold monomer V2.0 prediction for D-ribose pyranase (Q2G1A5) · a predicted model of the same protein · chain B against A, TM-score 0.98

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 Q2G1A5
Elsewhere: RCSB PDB 3P13 · PDBe 3P13 · UniProt Q2G1A5

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