Research workbench
Crystal structure of the complex of murine gamma-herpesvirus 68 BCL-2 homolog M11 and a beclin 1 BH3 domain-derived peptide
Analyse Crystal structure of the complex of murine gamma-herpesvirus 68 BCL-2 homolog… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MI8
- Type
- protein
- Length
- 313 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- BCL-2 homolog (gene 16?); Beclin-1
- UniProt
- P89884, Q14457
- Ligands
- SO4
- Pockets
- 1 · best druggability 0.33
Structure
x-ray diffraction · 4 distinct chains · 72% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | BCL-2 homolog (gene 16?) | protein | 135 | 73% helix, 1% strand | P89884 |
| B | BCL-2 homolog (gene 16?) | protein | 136 | 71% helix, 1% strand | P89884 |
| C | Beclin-1 | protein | 20 | 75% helix, 0% strand | Q14457 |
| D | Beclin-1 | protein | 22 | 73% helix, 0% strand | Q14457 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 90 | 0.33 | 0.73 | 17 | empty |
Interfaces
3 interfaces between chains.
- B–D · 968 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 915 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 505 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4MI8 · Crystal structure of the complex of murine gamma-herpesvirus 68 Bcl-2 homolog M11 and a… · the same entry in another collection · chain A against A, TM-score 1.00
- Q14457 · AlphaFold monomer V2.0 prediction for beclin-1 (Q14457) · a predicted model of the same protein · chain D against A, TM-score 0.70
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 P89884
- Every structure of UniProt Q14457
- Elsewhere: RCSB PDB 4MI8 · PDBe 4MI8 · UniProt P89884 · UniProt Q14457
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