MolNFT v1 · #24430 · protein
Naphthalene 1,2-dioxygenase with nitric oxide bound in the active site.
1UUW · Naphthalene 1,2-dioxygenase alpha subunit: “Naphthalene 1,2-dioxygenase with nitric oxide bound in the active site.”. X-ray diffraction, 4 ligands (FES, FE, SO4), 5 pockets (best druggability 0.72). MolNFT v1 #24430 on GenesisL1: 3D…
- PDB
- 1UUW
- Type
- protein
- Length
- 640 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Naphthalene 1,2-dioxygenase alpha subunit; Naphthalene 1,2-dioxygenase beta subunit
- EC
- 1.14.12.12
- UniProt
- P0A110, P0A112
- Ligands
- FES, FE, SO4, NO
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Naphthalene 1,2-dioxygenase alpha subunit (EC 1.14.12.12) | protein | 447 | 34% helix, 25% strand | P0A110 |
| B | Naphthalene 1,2-dioxygenase beta subunit (EC 1.14.12.12) | protein | 193 | 27% helix, 37% strand | P0A112 |
Ligands and binding sites
- FES · Fe2/s2 (inorganic) cluster · ligand · chains A
- FE · Fe (III) ion · metal · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains B
- NO · Nitric oxide · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 177 | 0.72 | 0.89 | 31 | NO |
| 2 | 126 | 0.72 | 0.92 | 31 | empty |
| 3 | 161 | 0.54 | 0.80 | 36 | empty |
| 4 | 176 | 0.46 | 0.75 | 22 | empty |
| 5 | 56 | 0.30 | 0.76 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 1830 Ų buried · 43 hydrogen bonds · protein-protein
Compared structures
- 1UUW · Naphthalene 1,2-dioxygenase with nitric oxide bound in the active site. · the same entry in another collection · chain A against A, TM-score 1.00
- P0A110 · AlphaFold monomer V2.0 prediction for naphthalene 1,2-dioxygenase system, large oxygenase… · a predicted model of the same protein · chain A against A, TM-score 0.99
- P0A112 · AlphaFold monomer V2.0 prediction for naphthalene 1,2-dioxygenase system, small oxygenase… · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P0A110
- Every structure of UniProt P0A112
- Elsewhere: RCSB PDB 1UUW · PDBe 1UUW · UniProt P0A110 · UniProt P0A112
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