Research workbench
Naphthalene 1,2-dioxygenase with indole bound in the active site.
Analyse Naphthalene 1,2-dioxygenase with indole bound in the active site. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1EG9
- Type
- protein
- Length
- 640 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (naphthalene 1,2-dioxygenase alpha subunit); Protein (naphthalene 1,2-dioxygenase…
- EC
- 1.14.12.12
- UniProt
- P0A110, P0A112
- Ligands
- FES, IND, FE, SO4
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein (naphthalene 1,2-dioxygenase alpha subunit) (EC 1.14.12.12) | protein | 447 | 35% helix, 25% strand | P0A110 |
| B | Protein (naphthalene 1,2-dioxygenase beta subunit) (EC 1.14.12.12) | protein | 193 | 27% helix, 36% strand | P0A112 |
Ligands and binding sites
- FES · Fe2/s2 (inorganic) cluster · ligand · chains A
- IND · Indole · ligand · chains A
- FE · Fe (III) ion · metal · chains A
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
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 | 191 | 0.70 | 0.87 | 34 | IND |
| 2 | 94 | 0.69 | 0.94 | 24 | empty |
| 3 | 179 | 0.57 | 0.81 | 39 | empty |
| 4 | 169 | 0.46 | 0.76 | 22 | empty |
| 5 | 58 | 0.29 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1838 Ų buried · 44 hydrogen bonds · protein-protein
Compared structures
- 1EG9 · Naphthalene 1,2-dioxygenase with indole 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 1EG9 · PDBe 1EG9 · UniProt P0A110 · UniProt P0A112
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