MolNFT v1 · #17031 · protein

The structure of bacillus subtilis rbsd complexed with D-ribose

1OGD · High affinity ribose transport protein rbsd: “The structure of bacillus subtilis rbsd complexed with D-ribose”. X-ray diffraction, 2 ligands (RIP, CL), 20 pockets (best druggability 0.52). MolNFT v1 #17031 on GenesisL1: 3D…

PDB: 1OGD
Type: protein
Length: 655 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: High affinity ribose transport protein rbsd
UniProt: P36946
Ligands: RIP, CL
Pockets: 20 · best druggability 0.52

Structure

x-ray diffraction · 1 distinct chain · 34% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E	High affinity ribose transport protein rbsd	protein	131	34% helix, 24% strand	P36946

Ligands and binding sites

RIP · beta-D-ribopyranose · ligand · 5 copies · chains A, E, B, C, D
CL · Chloride ion · ion · 2 copies · chains A, D

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

Pockets

20 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	164	0.52	0.79	27	empty
2	182	0.52	0.78	24	empty
3	153	0.50	0.78	23	empty
4	177	0.49	0.77	26	empty
5	160	0.48	0.77	26	empty

Interfaces

5 interfaces between chains.

A–B · 415 Å² buried · 4 hydrogen bonds · protein-protein
B–C · 414 Å² buried · 3 hydrogen bonds · protein-protein
D–E · 413 Å² buried · 3 hydrogen bonds · protein-protein
A–E · 411 Å² buried · 3 hydrogen bonds · protein-protein
C–D · 411 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

1OGD · The Structure of Bacillus subtilis RbsD complexed with D-ribose · the same entry in another collection · chain A against A, TM-score 1.00
P36946 · AlphaFold monomer V2.0 prediction for D-ribose pyranase (P36946) · a predicted model of the same protein · chain A 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 P36946
Elsewhere: RCSB PDB 1OGD · PDBe 1OGD · UniProt P36946

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