Research workbench
Crystal structure of biphenyl 2,3-dioxygenase from sphingomonas yanoikuyae B1
Analyse Crystal structure of biphenyl 2,3-dioxygenase from sphingomonas yanoikuyae B1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GBW
- Type
- protein
- Length
- 1,854 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Biphenyl 2,3-dioxygenase alpha subunit; Biphenyl 2,3-dioxygenase beta subunit
- UniProt
- A2TC87, A2TC88
- Ligands
- FES, FE, OXY
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Biphenyl 2,3-dioxygenase alpha subunit | protein | 449 | 35% helix, 25% strand | A2TC87 |
| B, D, F | Biphenyl 2,3-dioxygenase beta subunit | protein | 170 | 23% helix, 44% strand | A2TC88 |
| C | Biphenyl 2,3-dioxygenase alpha subunit | protein | 446 | 36% helix, 25% strand | A2TC87 |
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
- OXY · Oxygen molecule · ion · 3 copies · chains A, E, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 370 | 0.81 | 0.90 | 43 | empty |
| 2 | 90 | 0.77 | 0.98 | 20 | OXY |
| 3 | 93 | 0.77 | 0.97 | 21 | OXY |
| 4 | 838 | 0.76 | 0.80 | 93 | empty |
| 5 | 74 | 0.75 | 0.98 | 20 | OXY |
Interfaces
12 interfaces between chains.
- A–B · 1765 Ų buried · 36 hydrogen bonds · protein-protein
- E–F · 1699 Ų buried · 38 hydrogen bonds · protein-protein
- C–D · 1677 Ų buried · 38 hydrogen bonds · protein-protein
- C–E · 1652 Ų buried · 31 hydrogen bonds · protein-protein
- A–C · 1602 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 2GBW · Crystal Structure of Biphenyl 2,3-Dioxygenase from Sphingomonas yanoikuyae B1 · 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 A2TC87
- Every structure of UniProt A2TC88
- Elsewhere: RCSB PDB 2GBW · PDBe 2GBW · UniProt A2TC87 · UniProt A2TC88
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