Research workbench
Napthalene 1,2-dioxygenase
Analyse Napthalene 1,2-dioxygenase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NDO
- Type
- protein
- Length
- 1,918 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Napthalene 1,2-dioxygenase
- EC
- 1.14.12.12
- UniProt
- P0A110, P0A112
- Ligands
- FES, FE
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Napthalene 1,2-dioxygenase (EC 1.14.12.12) | protein | 447 | 35% helix, 25% strand | P0A110 |
| B, D, F | Napthalene 1,2-dioxygenase (EC 1.14.12.12) | protein | 193 | 27% helix, 37% strand | P0A112 |
| E | Napthalene 1,2-dioxygenase (EC 1.14.12.12) | protein | 445 | 33% helix, 25% strand | P0A110 |
Ligands and binding sites
- FES · Fe2/s2 (inorganic) cluster · ligand · 3 copies · chains A, C, E
- FE · Fe (III) ion · metal · 3 copies · chains A, C, E
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 | 1164 | 0.82 | 0.83 | 115 | empty |
| 2 | 570 | 0.80 | 0.86 | 40 | empty |
| 3 | 835 | 0.80 | 0.83 | 94 | empty |
| 4 | 752 | 0.77 | 0.82 | 77 | empty |
| 5 | 191 | 0.76 | 0.91 | 39 | empty |
Interfaces
12 interfaces between chains.
- E–F · 1849 Ų buried · 43 hydrogen bonds · protein-protein
- A–B · 1819 Ų buried · 40 hydrogen bonds · protein-protein
- C–D · 1819 Ų buried · 43 hydrogen bonds · protein-protein
- B–F · 1601 Ų buried · 20 hydrogen bonds · protein-protein
- D–F · 1595 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 1NDO · Naphthalene 1,2-dioxygenase · the same entry in another collection · chain F against F, 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 E 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 1NDO · PDBe 1NDO · UniProt P0A110 · UniProt P0A112
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