MolNFT v1 · #94084 · protein
Naphthalene 1,2-dioxygenase bound to 1-indanone
4HM1 · Naphthalene 1,2-dioxygenase subunit alpha: “Naphthalene 1,2-dioxygenase bound to 1-indanone”. X-ray diffraction, 4 ligands (FES, 1ON, FE), 5 pockets (best druggability 0.78). MolNFT v1 #94084 on GenesisL1: 3D structure, binding…
- PDB
- 4HM1
- Type
- protein
- Length
- 638 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Naphthalene 1,2-dioxygenase subunit alpha; Naphthalene 1,2-dioxygenase subunit beta
- EC
- 1.14.12.12
- UniProt
- P0A111, P0A113
- Ligands
- FES, 1ON, FE, SO4
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Naphthalene 1,2-dioxygenase subunit alpha (EC 1.14.12.12) | protein | 446 | 35% helix, 25% strand | P0A111 |
| B | Naphthalene 1,2-dioxygenase subunit beta (EC 1.14.12.12) | protein | 192 | 29% helix, 37% strand | P0A113 |
Ligands and binding sites
- FES · Fe2/s2 (inorganic) cluster · ligand · chains A
- 1ON · 2,3-dihydro-1H-inden-1-one · ligand · chains A
- FE · Fe (III) ion · metal · chains A
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 8 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 | 132 | 0.78 | 0.96 | 24 | 1ON |
| 2 | 91 | 0.70 | 0.94 | 24 | empty |
| 3 | 155 | 0.54 | 0.81 | 36 | empty |
| 4 | 183 | 0.48 | 0.76 | 24 | empty |
| 5 | 64 | 0.30 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1813 Ų buried · 42 hydrogen bonds · protein-protein
Compared structures
- 4HM1 · Naphthalene 1,2-Dioxygenase bound to 1-inda · 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 4HM1 · PDBe 4HM1 · UniProt P0A111 · UniProt P0A113
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