MolNFT v1 · #63065 · protein
Structure from the mobile metagenome of V. pseudocholerae. VPC_CASS1
3EY8 · Biphenyl-2,3-diol 1,2-dioxygenase III-related protein: “Structure from the mobile metagenome of V. pseudocholerae. VPC_CASS1”. X-ray diffraction, 1 ligand (SO4), 2 pockets (best druggability 0.73). MolNFT v1 #63065 on GenesisL1: 3D…
- PDB
- 3EY8
- Type
- protein
- Length
- 260 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Biphenyl-2,3-diol 1,2-dioxygenase III-related protein
- UniProt
- Q9K3D3
- Ligands
- SO4
- Pockets
- 2 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 17% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Biphenyl-2,3-diol 1,2-dioxygenase III-related protein | protein | 129 | 17% helix, 43% strand | Q9K3D3 |
| B | Biphenyl-2,3-diol 1,2-dioxygenase III-related protein | protein | 131 | 17% helix, 43% strand | Q9K3D3 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 131 | 0.73 | 0.92 | 47 | empty |
| 2 | 139 | 0.59 | 0.84 | 19 | SO4 |
Interfaces
1 interface between chains.
- A–B · 2692 Ų buried · 41 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 modified (engineered).
Compared structures
- 3EY8 · Structure from the mobile metagenome of V. Pseudocholerae. VPC_CASS1 · 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 Q9K3D3
- Elsewhere: RCSB PDB 3EY8 · PDBe 3EY8 · UniProt Q9K3D3
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