MolNFT v1 · #52267 · protein
Crystal structure of mycobacterium tuberculosis ribose-5- phosphate isomerase B in complex with the inhibitor 5- deoxy-5-phospho-D-ribonate
2VVQ · Ribose-5-phosphate isomerase B: “Crystal structure of mycobacterium tuberculosis ribose-5- phosphate isomerase B in complex with the inhibitor…”. X-ray diffraction, 2 ligands (R10, SO4), 8 pockets (best druggability 0.80). MolNFT v1…
- PDB
- 2VVQ
- Type
- protein
- Length
- 783 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
- R10, SO4
- Pockets
- 8 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E | Ribose-5-phosphate isomerase B (EC 5.3.1.6) | protein | 156 | 47% helix, 15% strand | Q79FD7 |
| C | Ribose-5-phosphate isomerase B (EC 5.3.1.6) | protein | 158 | 49% helix, 15% strand | Q79FD7 |
| D | Ribose-5-phosphate isomerase B (EC 5.3.1.6) | protein | 157 | 46% helix, 15% strand | Q79FD7 |
Ligands and binding sites
- R10 · 5-O-phosphono-D-ribonic acid · ligand · 5 copies · chains A, B, C, D, E
- SO4 · Sulfate ion · ion · 2 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1171 | 0.80 | 0.81 | 95 | empty |
| 2 | 305 | 0.58 | 0.77 | 53 | SO4 |
| 3 | 76 | 0.58 | 0.89 | 20 | R10 |
| 4 | 65 | 0.58 | 0.90 | 19 | R10 |
| 5 | 60 | 0.55 | 0.89 | 20 | R10 |
Interfaces
6 interfaces between chains.
- C–D · 2154 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 2113 Ų buried · 33 hydrogen bonds · protein-protein
- B–D · 504 Ų buried · 5 hydrogen bonds · protein-protein
- D–E · 146 Ų buried · 2 hydrogen bonds · protein-protein
- B–E · 103 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 2VVQ · 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 2VVQ · PDBe 2VVQ · UniProt Q79FD7
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