MolNFT v1 · #139305 · protein
Oxygenase component of 3-nitrotoluene dioxygenase from diaphorobacter sp. strain DS2
5XBP · 3NT oxygenase alpha subunit: “Oxygenase component of 3-nitrotoluene dioxygenase from diaphorobacter sp. strain DS2”. X-ray diffraction, 2 ligands (FES, FE), 20 pockets (best druggability 0.84). MolNFT v1 #139305 on GenesisL1: 3D…
- PDB
- 5XBP
- Type
- protein
- Length
- 1,908 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3NT oxygenase alpha subunit; 3NT oxygenase beta subunit
- UniProt
- M9PW10, M9PV03
- Ligands
- FES, FE
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G | 3NT oxygenase alpha subunit | protein | 444 | 36% helix, 25% strand | M9PW10 |
| C, F, I | 3NT oxygenase beta subunit | protein | 192 | 26% helix, 37% strand | M9PV03 |
Ligands and binding sites
- FES · Fe2/s2 (inorganic) cluster · ligand · 3 copies · chains A, D, G
- FE · Fe (III) ion · metal · 3 copies · chains A, D, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 843 | 0.84 | 0.86 | 103 | empty |
| 2 | 109 | 0.79 | 0.98 | 23 | empty |
| 3 | 96 | 0.79 | 0.99 | 23 | empty |
| 4 | 84 | 0.77 | 0.98 | 17 | empty |
| 5 | 661 | 0.76 | 0.82 | 69 | empty |
Interfaces
12 interfaces between chains.
- A–C · 1935 Ų buried · 40 hydrogen bonds · protein-protein
- G–I · 1913 Ų buried · 43 hydrogen bonds · protein-protein
- D–F · 1891 Ų buried · 40 hydrogen bonds · protein-protein
- C–I · 1632 Ų buried · 21 hydrogen bonds · protein-protein
- F–I · 1619 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 5XBP · Oxygenase component of 3-nitrotoluene dioxygenase from Diaphorobacter sp. strain DS2 · 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 M9PW10
- Every structure of UniProt M9PV03
- Elsewhere: RCSB PDB 5XBP · PDBe 5XBP · UniProt M9PW10 · UniProt M9PV03
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