Research workbench
The crystal structure of nitrobenzene dioxygenase in complex with 3- nitrotoluene
Analyse The crystal structure of nitrobenzene dioxygenase in complex with 3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2BMR
- Type
- protein
- Length
- 631 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oxygenase-alpha nbdo; Oxygenase-beta nbdo
- UniProt
- Q8RTL4, Q8RTL3
- Ligands
- FES, 3NT, NI, FE
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Oxygenase-alpha nbdo | protein | 437 | 36% helix, 26% strand | Q8RTL4 |
| B | Oxygenase-beta nbdo | protein | 194 | 28% helix, 37% strand | Q8RTL3 |
Ligands and binding sites
- FES · Fe2/s2 (inorganic) cluster · ligand · chains A
- 3NT · 3-nitrotoluene · ligand · chains A
- NI · Nickel (II) ion · metal · 2 copies · chains B
- FE · Fe (III) ion · metal · chains A
- EOH · Ethanol · additive · 9 copies · chains A, B
- 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 71 | 0.75 | 0.99 | 19 | 3NT |
| 2 | 72 | 0.73 | 0.97 | 25 | EDO |
| 3 | 165 | 0.56 | 0.81 | 33 | EDO, EOH |
| 4 | 178 | 0.50 | 0.77 | 25 | empty |
| 5 | 176 | 0.44 | 0.74 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 1904 Ų buried · 44 hydrogen bonds · protein-protein
Compared structures
- 2BMR · The Crystal Structure of Nitrobenzene Dioxygenase in complex with 3- nitrotoluene · 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 Q8RTL4
- Every structure of UniProt Q8RTL3
- Elsewhere: RCSB PDB 2BMR · PDBe 2BMR · UniProt Q8RTL4 · UniProt Q8RTL3
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