Research workbench
Crystal structure of cis-biphenyl-2,3-dihydrodiol-2,3- dehydrogenase (BPHB)FROM pandoraea pnomenusa strain B- 356 in intermediate state of substrate binding loop
Analyse Crystal structure of cis-biphenyl-2,3-dihydrodiol-2,3- dehydrogenase (BPHB)FROM… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZV3
- Type
- protein
- Length
- 534 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
- 4 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 44% 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 | 259 | 44% helix, 14% strand | Q46381 |
| B | Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase (EC 1.3.1.56) | protein | 275 | 44% helix, 13% strand | Q46381 |
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 457 | 0.74 | 0.83 | 50 | empty |
| 2 | 436 | 0.64 | 0.78 | 49 | empty |
| 3 | 63 | 0.44 | 0.83 | 19 | empty |
| 4 | 94 | 0.39 | 0.77 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 2106 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 3ZV3 · 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 A 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 3ZV3 · PDBe 3ZV3 · UniProt Q46381
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