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Crystal structure of D-ribose pyranase SA240

Analyse Crystal structure of D-ribose pyranase SA240 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3P12
Type: protein
Length: 516 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: D-ribose pyranase
EC: 5.5.1.-
UniProt: Q2G1A5
Pockets: 3 · best druggability 0.67

Structure

x-ray diffraction · 3 distinct chains · 30% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	D-ribose pyranase (EC 5.5.1.-)	protein	129	31% helix, 26% strand	Q2G1A5
C	D-ribose pyranase (EC 5.5.1.-)	protein	130	31% helix, 25% strand	Q2G1A5
D	D-ribose pyranase (EC 5.5.1.-)	protein	128	30% helix, 26% strand	Q2G1A5

Ligands and binding sites

GOL · Glycerol · additive · 4 copies · chains A, B, C, D

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

Pockets

3 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	600	0.67	0.77	77	empty
2	168	0.51	0.79	21	empty
3	162	0.47	0.76	21	empty

Interfaces

4 interfaces between chains.

B–C · 811 Å² buried · 14 hydrogen bonds · protein-protein
A–D · 786 Å² buried · 11 hydrogen bonds · protein-protein
B–D · 342 Å² buried · 1 hydrogen bond · protein-protein
A–C · 331 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

3P12 · Crystal Structure of D-ribose Pyranase Sa240 · the same entry in another collection · chain D against D, TM-score 1.00
Q2G1A5 · AlphaFold monomer V2.0 prediction for D-ribose pyranase (Q2G1A5) · a predicted model of the same protein · chain D 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 3P12 · PDBe 3P12 · UniProt Q2G1A5

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