Research workbench
RV2002 gene product from mycobacterium tuberculosis
Analyse RV2002 gene product from mycobacterium tuberculosis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NFQ
- Type
- protein
- Length
- 976 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative oxidoreductase RV2002
- EC
- 1.1.1.53
- UniProt
- P69167
- Ligands
- NAI, AOI
- Pockets
- 8 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Putative oxidoreductase RV2002 (EC 1.1.1.53) | protein | 244 | 45% helix, 19% strand | P69167 |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- AOI · Androsterone · ligand · 4 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 779 | 0.86 | 0.89 | 63 | empty |
| 2 | 481 | 0.76 | 0.84 | 59 | NAI, AOI |
| 3 | 423 | 0.75 | 0.84 | 48 | NAI, AOI |
| 4 | 425 | 0.75 | 0.84 | 47 | NAI, AOI |
| 5 | 442 | 0.75 | 0.84 | 46 | NAI, AOI |
Interfaces
6 interfaces between chains.
- B–C · 1659 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 1657 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1476 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1462 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 779 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 1NFQ · Rv2002 gene product from Mycobacterium tuberculosis · 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 P69167
- Elsewhere: RCSB PDB 1NFQ · PDBe 1NFQ · UniProt P69167
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