MolNFT v1 · #31655 · protein
Crystal structure of naphthalene 1,2-dioxygenase from rhodococcus sp.
2B1X · Naphthalene dioxygenase large subunit: “Crystal structure of naphthalene 1,2-dioxygenase from rhodococcus sp.”. X-ray diffraction, 2 ligands (FES, FE), 20 pockets (best druggability 0.81). MolNFT v1 #31655 on GenesisL1: 3D…
- PDB
- 2B1X
- Type
- protein
- Length
- 1,824 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Naphthalene dioxygenase large subunit; Naphthalene dioxygenase small subunit
- EC
- 1.14.12.12
- UniProt
- Q9X3R9, Q9WVZ0
- Ligands
- FES, FE
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Naphthalene dioxygenase large subunit (EC 1.14.12.12) | protein | 441 | 31% helix, 25% strand | Q9X3R9 |
| B, D, F | Naphthalene dioxygenase small subunit (EC 1.14.12.12) | protein | 167 | 22% helix, 44% strand | Q9WVZ0 |
Ligands and binding sites
- FES · Fe2/s2 (inorganic) cluster · ligand · 3 copies · chains A, C, E
- FE · Fe (III) ion · metal · 3 copies · chains A, C, E
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 13 copies · chains A, B, C, E, F, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 520 | 0.81 | 0.87 | 38 | empty |
| 2 | 91 | 0.78 | 0.98 | 20 | MPD |
| 3 | 90 | 0.77 | 0.98 | 20 | MPD |
| 4 | 85 | 0.76 | 0.98 | 19 | MPD |
| 5 | 330 | 0.72 | 0.85 | 52 | MPD |
Interfaces
12 interfaces between chains.
- E–F · 1873 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 1870 Ų buried · 32 hydrogen bonds · protein-protein
- C–D · 1869 Ų buried · 32 hydrogen bonds · protein-protein
- C–E · 1659 Ų buried · 33 hydrogen bonds · protein-protein
- A–E · 1654 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 2B1X · Crystal structure of naphthalene 1,2-dioxygenase from Rhodococcus sp. · 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 Q9X3R9
- Every structure of UniProt Q9WVZ0
- Elsewhere: RCSB PDB 2B1X · PDBe 2B1X · UniProt Q9X3R9 · UniProt Q9WVZ0
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