Research workbench
Structure of the epstein-barr virus GPCR BILF1 in complex with human gi
Analyse Structure of the epstein-barr virus GPCR BILF1 in complex with human gi in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7JHJ
- Type
- protein
- Length
- 1,117 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Guanine nucleotide-binding protein G(I) subunit alpha-1; Guanine nucleotide-binding…
- UniProt
- P63096, P62873, P59768, Q3KSP2
- Ligands
- Y01
- Pockets
- 13 · best druggability 0.82
Structure
electron microscopy · 5 distinct chains · 29% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanine nucleotide-binding protein G(I) subunit alpha-1 | protein | 218 | 39% helix, 18% strand | P63096 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 336 | 7% helix, 43% strand | P62873 |
| C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 53 | 51% helix, 0% strand | P59768 |
| D | Antibody fragment SCFV16 | protein | 233 | 1% helix, 48% strand | — |
| R | BILF1 | protein | 277 | 68% helix, 2% strand | Q3KSP2 |
Ligands and binding sites
- Y01 · Cholesterol hemisuccinate · ligand · chains R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 776 | 0.82 | 0.85 | 66 | empty |
| 2 | 569 | 0.81 | 0.86 | 52 | empty |
| 3 | 990 | 0.72 | 0.76 | 67 | empty |
| 4 | 375 | 0.63 | 0.79 | 63 | empty |
| 5 | 139 | 0.59 | 0.84 | 28 | empty |
Interfaces
6 interfaces between chains.
- B–C · 1944 Ų buried · 14 hydrogen bonds · protein-protein
- A–R · 1210 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 1133 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 631 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 428 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7JHJ · Structure of the Epstein-Barr virus GPCR BILF1 in complex with human Gi · the same entry in another collection · chain R against R, TM-score 1.00
- P62873 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(I)/G(S)/G(T)… · a predicted model of the same protein · chain B against A, TM-score 1.00
- P59768 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(I)/G(S)/G(O)… · a predicted model of the same protein · chain C against A, TM-score 0.94
- P63096 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(I) subunit… · a predicted model of the same protein · chain A against A, TM-score 0.84
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 P63096
- Every structure of UniProt P62873
- Every structure of UniProt P59768
- Every structure of UniProt Q3KSP2
- Elsewhere: RCSB PDB 7JHJ · PDBe 7JHJ · UniProt P63096 · UniProt P62873 · UniProt P59768 · UniProt Q3KSP2
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