Research workbench
Naphthalene 1,2-dioxygenase, binary complex with dioxygen
Analyse Naphthalene 1,2-dioxygenase, binary complex with dioxygen in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1O7M
- 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
- FES, FE, SO4, OXY
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 28% 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
- FES · Fe2/s2 (inorganic) cluster · ligand · chains A
- FE · Fe (III) ion · metal · chains A
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- OXY · Oxygen molecule · ion · chains A
- 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 219 | 0.71 | 0.87 | 38 | OXY, FE |
| 2 | 51 | 0.70 | 0.98 | 21 | empty |
| 3 | 96 | 0.68 | 0.93 | 23 | empty |
| 4 | 160 | 0.53 | 0.80 | 35 | EDO |
| 5 | 161 | 0.45 | 0.76 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1844 Ų buried · 43 hydrogen bonds · protein-protein
Compared structures
- 1O7M · Naphthalene 1,2-dioxygenase, binary complex with dioxygen · 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 1O7M · PDBe 1O7M · UniProt P23094 · UniProt P23095
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