MolNFT v1 · #15795 · protein
RV2002 gene product from mycobacterium tuberculosis
1NFR · Putative oxidoreductase RV2002: “RV2002 gene product from mycobacterium tuberculosis”. X-ray diffraction, 1 ligand (NAD), 9 pockets (best druggability 0.86). MolNFT v1 #15795 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1NFR
- 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
- NAD
- Pockets
- 9 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 47% 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 | 47% helix, 19% strand | P69167 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 726 | 0.86 | 0.89 | 60 | empty |
| 2 | 402 | 0.76 | 0.85 | 46 | NAD |
| 3 | 376 | 0.76 | 0.86 | 43 | NAD |
| 4 | 438 | 0.75 | 0.84 | 58 | NAD |
| 5 | 397 | 0.75 | 0.84 | 48 | NAD |
Interfaces
6 interfaces between chains.
- A–D · 1632 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1619 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1485 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1463 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 772 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 1NFR · Rv2002 gene product from Mycobacterium tuberculosis · the same entry in another collection · chain C against C, 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 1NFR · PDBe 1NFR · UniProt P69167
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