Research workbench
E.COLI dsbb C104S with ubiquinone
Analyse E.COLI dsbb C104S with ubiquinone in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WVF
- Type
- protein
- Length
- 386 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Green fluorescent PROTEIN,DISULFIDE bond formation protein B,GREEN fluorescent protein
- UniProt
- P42212, P0A6M2
- Ligands
- CRO, UQ1
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Green fluorescent PROTEIN,DISULFIDE bond formation protein B,GREEN fluorescent protein | protein | 386 | 33% helix, 32% strand | P42212, P0A6M2 |
Ligands and binding sites
- CRO · {2-[(1R,2R)-1-amino-2-hydroxypropyl]-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid · ligand · chains A
- UQ1 · Ubiquinone-1 · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 126 | 0.78 | 0.96 | 30 | CRO |
| 2 | 235 | 0.75 | 0.89 | 28 | UQ1 |
| 3 | 106 | 0.44 | 0.78 | 16 | empty |
| 4 | 115 | 0.44 | 0.78 | 18 | empty |
| 5 | 72 | 0.32 | 0.74 | 18 | empty |
Modifications
Observed in the structure: 2 cofactor, 1 disulfide (chromophore, disulfide).
Compared structures
- 6WVF · E.coli DsbB C104S with ubiqui · the same entry in another collection · chain A against A, TM-score 1.00
- P42212 · AlphaFold monomer V2.0 prediction for green fluorescent protein (P42212) · a predicted model of the same protein · chain A against A, TM-score 0.58
- P0A6M2 · AlphaFold monomer V2.0 prediction for disulfide bond formation protein B (P0A6M2) · a predicted model of the same protein · chain A against A, TM-score 0.41
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 P42212
- Every structure of UniProt P0A6M2
- Elsewhere: RCSB PDB 6WVF · PDBe 6WVF · UniProt P42212 · UniProt P0A6M2
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