Research workbench
Crystal structure of a computationally designed inhibitor of an epstein-barr viral BCL-2 protein
Analyse Crystal structure of a computationally designed inhibitor of an epstein-barr… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4OYD
- Type
- protein
- Length
- 548 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Apoptosis regulator BHRF1; Computationally designed inhibitor
- UniProt
- P0C6Z1
- Pockets
- 7 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 77% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Apoptosis regulator BHRF1 | protein | 156 | 72% helix, 0% strand | P0C6Z1 |
| B, D | Computationally designed inhibitor | protein | 117 | 88% helix, 0% strand | — |
| C | Apoptosis regulator BHRF1 | protein | 158 | 73% helix, 0% strand | P0C6Z1 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 223 | 0.56 | 0.79 | 25 | empty |
| 2 | 212 | 0.54 | 0.78 | 29 | empty |
| 3 | 243 | 0.52 | 0.76 | 30 | empty |
| 4 | 64 | 0.50 | 0.85 | 22 | empty |
| 5 | 147 | 0.45 | 0.76 | 20 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1396 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1352 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 666 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 274 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 65 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4OYD · Crystal structure of a computationally designed inhibitor of an Epstein-Barr viral Bcl-2… · 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 P0C6Z1
- Elsewhere: RCSB PDB 4OYD · PDBe 4OYD · UniProt P0C6Z1
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