Research workbench
Crystal structure of 2,3-dihydroxybiphenyl 1,2-dioxygenase (dhbd) complexed with 2',6'-dicl dihydroxybiphenyl (dhb)
Analyse Crystal structure of 2,3-dihydroxybiphenyl 1,2-dioxygenase (dhbd) complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1LKD
- Type
- protein
- Length
- 287 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Biphenyl-2,3-diol 1,2-dioxygenase
- EC
- 1.13.11.39
- UniProt
- P47228
- Ligands
- BP6, FE2
- Pockets
- 1 · best druggability 0.60
Structure
x-ray diffraction · 1 distinct chain · 20% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Biphenyl-2,3-diol 1,2-dioxygenase (EC 1.13.11.39) | protein | 287 | 20% helix, 41% strand | P47228 |
Ligands and binding sites
- BP6 · 2',6'-dichloro-biphenyl-2,6-diol · ligand · 2 copies · chains A
- FE2 · Fe (II) ion · metal · 2 copies · chains A
- P6G · Hexaethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 238 | 0.60 | 0.79 | 29 | FE2, BP6, P6G |
Compared structures
- 1LKD · Crystal structure of 2,3-dihydroxybiphenyl 1,2-dioxygenase (dhbd) complexed with… · the same entry in another collection · chain A against A, TM-score 1.00
- P47228 · AlphaFold monomer V2.0 prediction for biphenyl-2,3-diol 1,2-dioxygenase (P47228) · a predicted model of the same protein · chain A 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 P47228
- Elsewhere: RCSB PDB 1LKD · PDBe 1LKD · UniProt P47228
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