MolNFT v1 · #106325 · protein
The native structure of mycobacterial RV1454C complexed with NADPH
4RVU · Probable quinone reductase qor (NADPH:QUINONE reductase)…: “The native structure of mycobacterial RV1454C complexed with NADPH”. X-ray diffraction, 1 ligand (NDP), 15 pockets (best druggability 0.81). MolNFT v1 #106325 on GenesisL1…
- PDB
- 4RVU
- Type
- protein
- Length
- 1,308 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable quinone reductase qor (NADPH:QUINONE reductase) (zeta-crystallin homolog protein)
- UniProt
- O53146
- Ligands
- NDP
- Pockets
- 15 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable quinone reductase qor (NADPH:QUINONE reductase) (zeta-crystallin homolog protein) | protein | 329 | 36% helix, 27% strand | O53146 |
| B | Probable quinone reductase qor (NADPH:QUINONE reductase) (zeta-crystallin homolog protein) | protein | 328 | 35% helix, 28% strand | O53146 |
| C | Probable quinone reductase qor (NADPH:QUINONE reductase) (zeta-crystallin homolog protein) | protein | 328 | 34% helix, 27% strand | O53146 |
| D | Probable quinone reductase qor (NADPH:QUINONE reductase) (zeta-crystallin homolog protein) | protein | 323 | 34% helix, 28% strand | O53146 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 713 | 0.81 | 0.85 | 91 | NDP |
| 2 | 603 | 0.79 | 0.85 | 58 | NDP |
| 3 | 527 | 0.79 | 0.85 | 57 | NDP |
| 4 | 586 | 0.78 | 0.84 | 62 | NDP |
| 5 | 126 | 0.51 | 0.80 | 24 | empty |
Interfaces
5 interfaces between chains.
- A–D · 1266 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 1264 Ų buried · 24 hydrogen bonds · protein-protein
- B–D · 373 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 267 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 62 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4RVU · The native structure of mycobacterial Rv1454c complexed with NADPH · 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 O53146
- Elsewhere: RCSB PDB 4RVU · PDBe 4RVU · UniProt O53146
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