Research workbench
Crystal structure of cis-biphenyl-2,3-dihydrodiol-2,3- dehydrogenase (bphb) from pandoraea pnomenusa strain B- 356 complex with co-enzyme NAD and product 2,3- dihydroxybiphenyl
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
- 3ZV5
- Type
- protein
- Length
- 543 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
- Ligands
- NAD, BPY
- Pockets
- 3 · 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 | 275 | 48% helix, 13% strand | Q46381 |
| B | Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase (EC 1.3.1.56) | protein | 268 | 47% helix, 13% strand | Q46381 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- BPY · Biphenyl-2,3-diol · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 440 | 0.77 | 0.86 | 55 | NAD, BPY |
| 2 | 598 | 0.77 | 0.83 | 56 | NAD |
| 3 | 108 | 0.43 | 0.78 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 2083 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 3ZV5 · 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 0.99
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 Q46381
- Elsewhere: RCSB PDB 3ZV5 · PDBe 3ZV5 · UniProt Q46381
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