Research workbench
Crystal structure of human bak in complex with M3W5_BID
Analyse Crystal structure of human bak in complex with M3W5_BID in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7M5B
- Type
- protein
- Length
- 366 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- BCL-2 homologous ANTAGONIST/KILLER; BH3-interacting domain death agonist P15
- UniProt
- Q16611, P55957
- Ligands
- CU
- Pockets
- 5 · best druggability 0.52
Structure
x-ray diffraction · 4 distinct chains · 74% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | BCL-2 homologous ANTAGONIST/KILLER | protein | 157 | 73% helix, 1% strand | Q16611 |
| B | BH3-interacting domain death agonist P15 | protein | 25 | 80% helix, 8% strand | P55957 |
| C | BCL-2 homologous ANTAGONIST/KILLER | protein | 160 | 74% helix, 1% strand | Q16611 |
| D | BH3-interacting domain death agonist P15 | protein | 24 | 79% helix, 4% strand | P55957 |
Ligands and binding sites
- CU · Copper (II) ion · metal · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 133 | 0.52 | 0.81 | 23 | empty |
| 2 | 115 | 0.45 | 0.78 | 17 | empty |
| 3 | 191 | 0.42 | 0.73 | 32 | empty |
| 4 | 93 | 0.41 | 0.78 | 17 | empty |
| 5 | 52 | 0.29 | 0.75 | 16 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1205 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1160 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 211 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 177 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 109 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7M5B · Crystal Structure of human BAK in complex with M3W5_BID · the same entry in another collection · chain D against D, TM-score 1.00
- Q16611 · AlphaFold monomer V2.0 prediction for BCL-2 homologous ANTAGONIST/KILLER (Q16611) · a predicted model of the same protein · chain A against A, TM-score 0.97
- P55957 · AlphaFold monomer V2.0 prediction for BH3-interacting domain death agonist (P55957) · a predicted model of the same protein · chain B against A, TM-score 0.78
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 Q16611
- Every structure of UniProt P55957
- Elsewhere: RCSB PDB 7M5B · PDBe 7M5B · UniProt Q16611 · UniProt P55957
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.