Research workbench
Epstein-barr virus encoded BCL-2 homolog bhrf-1 in complex with bid BH3 peptide
Analyse Epstein-barr virus encoded BCL-2 homolog bhrf-1 in complex with bid BH3 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7P33
- Type
- protein
- Length
- 895 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Apoptosis regulator BHRF1; BH3-interacting domain death agonist P15
- UniProt
- P03182, P55957
- Ligands
- PO4
- Pockets
- 14 · best druggability 0.52
Structure
x-ray diffraction · 10 distinct chains · 74% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Apoptosis regulator BHRF1 | protein | 154 | 75% helix, 0% strand | P03182 |
| B | Apoptosis regulator BHRF1 | protein | 155 | 73% helix, 0% strand | P03182 |
| C | Apoptosis regulator BHRF1 | protein | 152 | 74% helix, 0% strand | P03182 |
| D | Apoptosis regulator BHRF1 | protein | 156 | 73% helix, 0% strand | P03182 |
| E | Apoptosis regulator BHRF1 | protein | 148 | 74% helix, 0% strand | P03182 |
| G | BH3-interacting domain death agonist P15 | protein | 31 | 81% helix, 0% strand | P55957 |
| H | BH3-interacting domain death agonist P15 | protein | 30 | 60% helix, 0% strand | P55957 |
| F | BH3-interacting domain death agonist P15 | protein | 20 | 80% helix, 0% strand | P55957 |
| I | BH3-interacting domain death agonist P15 | protein | 23 | 74% helix, 0% strand | P55957 |
| J | BH3-interacting domain death agonist P15 | protein | 26 | 81% helix, 0% strand | P55957 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 241 | 0.52 | 0.76 | 28 | empty |
| 2 | 183 | 0.52 | 0.78 | 37 | empty |
| 3 | 71 | 0.47 | 0.83 | 15 | empty |
| 4 | 92 | 0.45 | 0.80 | 20 | empty |
| 5 | 193 | 0.44 | 0.73 | 22 | empty |
Interfaces
16 interfaces between chains.
- A–G · 893 Ų buried · 9 hydrogen bonds · protein-protein
- E–J · 876 Ų buried · 5 hydrogen bonds · protein-protein
- B–F · 858 Ų buried · 6 hydrogen bonds · protein-protein
- D–I · 809 Ų buried · 4 hydrogen bonds · protein-protein
- C–H · 801 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 7P33 · Epstein-Barr virus encoded Bcl-2 homolog BHRF-1 in complex with Bid BH3 peptide · the same entry in another collection · chain D against D, TM-score 1.00
- P55957 · AlphaFold monomer V2.0 prediction for BH3-interacting domain death agonist (P55957) · a predicted model of the same protein · chain I against A, TM-score 0.67
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 P03182
- Every structure of UniProt P55957
- Elsewhere: RCSB PDB 7P33 · PDBe 7P33 · UniProt P03182 · UniProt P55957
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