MolNFT v1 · #31662 · protein
Crystal structure of naphthalene 1,2-dioxygenase from rhodococcus sp. bound to indole
2B24 · Naphthalene dioxygenase large subunit: “Crystal structure of naphthalene 1,2-dioxygenase from rhodococcus sp. bound to indole”. X-ray diffraction, 3 ligands (FES, IND, FE), 20 pockets (best druggability 0.82). MolNFT v1 #31662 on…
- PDB
- 2B24
- Type
- protein
- Length
- 1,815 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, IND, FE
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Naphthalene dioxygenase large subunit (EC 1.14.12.12) | protein | 440 | 30% helix, 24% strand | Q9X3R9 |
| B, D, F | Naphthalene dioxygenase small subunit (EC 1.14.12.12) | protein | 165 | 19% helix, 42% strand | Q9WVZ0 |
Ligands and binding sites
- FES · Fe2/s2 (inorganic) cluster · ligand · 3 copies · chains A, C, E
- IND · Indole · ligand · 3 copies · chains A, C, E
- FE · Fe (III) ion · metal · 3 copies · chains A, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 466 | 0.82 | 0.89 | 35 | empty |
| 2 | 622 | 0.79 | 0.84 | 98 | empty |
| 3 | 85 | 0.77 | 0.98 | 19 | IND |
| 4 | 81 | 0.77 | 0.98 | 19 | FE, IND |
| 5 | 77 | 0.75 | 0.98 | 18 | IND |
Interfaces
12 interfaces between chains.
- E–F · 1872 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 1842 Ų buried · 33 hydrogen bonds · protein-protein
- C–D · 1841 Ų buried · 33 hydrogen bonds · protein-protein
- A–C · 1729 Ų buried · 32 hydrogen bonds · protein-protein
- A–E · 1727 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 2B24 · Crystal structure of naphthalene 1,2-dioxygenase from Rhodococcus sp. bound to indole · 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 2B24 · PDBe 2B24 · UniProt Q9X3R9 · UniProt Q9WVZ0
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