Research workbench
Naphthalene 1,2-dioxygenase with naphthalene bound in the active site.
Analyse Naphthalene 1,2-dioxygenase with naphthalene 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
- 1O7G
- 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
- P23094, P23095
- Ligands
- NPY, FES, FE, SO4
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 33% 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 | 35% helix, 25% strand | P23094 |
| B | Naphthalene 1,2-dioxygenase beta subunit (EC 1.14.12.12) | protein | 193 | 29% helix, 37% strand | P23095 |
Ligands and binding sites
- NPY · Naphthalene · ligand · chains A
- FES · Fe2/s2 (inorganic) cluster · ligand · chains A
- FE · Fe (III) ion · metal · chains A
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 197 | 0.74 | 0.89 | 36 | NPY |
| 2 | 130 | 0.74 | 0.93 | 32 | EDO |
| 3 | 222 | 0.58 | 0.80 | 41 | empty |
| 4 | 168 | 0.46 | 0.75 | 20 | empty |
| 5 | 65 | 0.30 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1796 Ų buried · 45 hydrogen bonds · protein-protein
Compared structures
- 1O7G · Naphthalene 1,2-dioxygenase with naphthalene bound in the active site. · 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 P23094
- Every structure of UniProt P23095
- Elsewhere: RCSB PDB 1O7G · PDBe 1O7G · UniProt P23094 · UniProt P23095
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