Research workbench
Crystal structure of cis-biphenyl-2,3-dihydrodiol-2,3- dehydrogenase (bphb) from pandoraea pnomenusa strain B- 356 in apo form at 1.8 ångström
Analyse Crystal structure of cis-biphenyl-2,3-dihydrodiol-2,3- dehydrogenase (bphb)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZV4
- Type
- protein
- Length
- 533 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase
- EC
- 1.3.1.56
- UniProt
- Q46381
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase (EC 1.3.1.56) | protein | 265 | 45% helix, 14% strand | Q46381 |
| B | Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase (EC 1.3.1.56) | protein | 268 | 49% helix, 13% strand | Q46381 |
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 577 | 0.77 | 0.83 | 54 | empty |
| 2 | 595 | 0.71 | 0.79 | 52 | empty |
| 3 | 68 | 0.52 | 0.86 | 24 | empty |
| 4 | 132 | 0.43 | 0.76 | 27 | empty |
| 5 | 50 | 0.32 | 0.77 | 9 | empty |
Interfaces
1 interface between chains.
- A–B · 2080 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 3ZV4 · Crystal structure of cis-biphenyl-2,3-dihydrodiol-2,3-dehydrogenase (bphb) from pandoraea… · the same entry in another collection · chain A against A, TM-score 1.00
- Q46381 · AlphaFold monomer V2.0 prediction for cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase… · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q46381
- Elsewhere: RCSB PDB 3ZV4 · PDBe 3ZV4 · UniProt Q46381
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