Research workbench
Crystal structure of the naphthalene 1,2-dioxygenase F352V mutant bound to phenanthrene.
Analyse Crystal structure of the naphthalene 1,2-dioxygenase F352V mutant bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2HML
- Type
- protein
- Length
- 638 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
- P0A111, P0A113
- Ligands
- FES, PEY, FE, SO4
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Naphthalene 1,2-dioxygenase alpha subunit (EC 1.14.12.12) | protein | 446 | 35% helix, 25% strand | P0A111 |
| B | Naphthalene 1,2-dioxygenase beta subunit (EC 1.14.12.12) | protein | 192 | 30% helix, 37% strand | P0A113 |
Ligands and binding sites
- FES · Fe2/s2 (inorganic) cluster · ligand · chains A
- PEY · Phenanthrene · ligand · chains A
- FE · Fe (III) ion · metal · chains A
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 17 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 132 | 0.76 | 0.94 | 26 | PEY |
| 2 | 119 | 0.74 | 0.94 | 32 | EDO |
| 3 | 165 | 0.55 | 0.81 | 35 | EDO |
| 4 | 159 | 0.44 | 0.75 | 20 | empty |
| 5 | 68 | 0.33 | 0.76 | 18 | EDO |
Interfaces
1 interface between chains.
- A–B · 1800 Ų buried · 43 hydrogen bonds · protein-protein
Compared structures
- 2HML · Crystal Structure of the Naphthalene 1,2-Dioxygenase F352V Mutant Bound to Phenanthrene. · the same entry in another collection · chain A against A, TM-score 1.00
- P0A111 · 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
- P0A113 · 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 P0A111
- Every structure of UniProt P0A113
- Elsewhere: RCSB PDB 2HML · PDBe 2HML · UniProt P0A111 · UniProt P0A113
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