Research workbench
Crystal structure of mycobacterium tuberculosis ribose-5-phosphate isomerase B in complex with alpha D-allose 6-phosphate
Analyse Crystal structure of mycobacterium tuberculosis ribose-5-phosphate isomerase B… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VVO
- Type
- protein
- Length
- 780 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribose-5-phosphate isomerase B
- EC
- 5.3.1.6
- UniProt
- Q79FD7
- Ligands
- A6P
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Ribose-5-phosphate isomerase B (EC 5.3.1.6) | protein | 156 | 48% helix, 15% strand | Q79FD7 |
Ligands and binding sites
- A6P · 6-O-phosphono-alpha-D-allopyranose · ligand · 5 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 976 | 0.76 | 0.78 | 69 | empty |
| 2 | 1014 | 0.72 | 0.75 | 97 | empty |
| 3 | 72 | 0.56 | 0.88 | 20 | A6P |
| 4 | 78 | 0.53 | 0.86 | 17 | A6P |
| 5 | 70 | 0.52 | 0.86 | 17 | A6P |
Interfaces
6 interfaces between chains.
- A–B · 2072 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 2066 Ų buried · 32 hydrogen bonds · protein-protein
- A–C · 426 Ų buried · 3 hydrogen bonds · protein-protein
- C–E · 142 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 107 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 2VVO · Crystal structure of Mycobacterium tuberculosis ribose-5-phosphate isomerase B in complex… · the same entry in another collection · chain A against A, TM-score 1.00
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 Q79FD7
- Elsewhere: RCSB PDB 2VVO · PDBe 2VVO · UniProt Q79FD7
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