Research workbench
Crystal structure of bak L100A in complex with activating antibody fragments
Analyse Crystal structure of bak L100A in complex with activating antibody fragments in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LK4
- Type
- protein
- Length
- 1,501 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- BCL-2 homologous ANTAGONIST/KILLER; 7D10 antibody vl fragment; 7D10 antibody vh fragment
- UniProt
- Q16611
- Pockets
- 20 · best druggability 0.72
Structure
x-ray diffraction · 9 distinct chains · 34% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| P | BCL-2 homologous ANTAGONIST/KILLER | protein | 134 | 63% helix, 0% strand | Q16611 |
| Q | BCL-2 homologous ANTAGONIST/KILLER | protein | 137 | 64% helix, 0% strand | Q16611 |
| R | BCL-2 homologous ANTAGONIST/KILLER | protein | 150 | 63% helix, 0% strand | Q16611 |
| S | BCL-2 homologous ANTAGONIST/KILLER | protein | 158 | 66% helix, 0% strand | Q16611 |
| A, C, E, G | 7D10 antibody vl fragment | protein | 109 | 3% helix, 48% strand | — |
| B | 7D10 antibody vh fragment | protein | 122 | 5% helix, 49% strand | — |
| D | 7D10 antibody vh fragment | protein | 123 | 7% helix, 48% strand | — |
| F | 7D10 antibody vh fragment | protein | 120 | 5% helix, 50% strand | — |
| H | 7D10 antibody vh fragment | protein | 121 | 2% helix, 49% strand | — |
Ligands and binding sites
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 7 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 555 | 0.72 | 0.81 | 40 | empty |
| 2 | 812 | 0.71 | 0.76 | 63 | empty |
| 3 | 677 | 0.67 | 0.76 | 73 | empty |
| 4 | 622 | 0.65 | 0.76 | 78 | empty |
| 5 | 408 | 0.63 | 0.77 | 50 | empty |
Interfaces
24 interfaces between chains.
- Q–S · 1600 Ų buried · 16 hydrogen bonds · protein-protein
- P–R · 1496 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 811 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 806 Ų buried · 6 hydrogen bonds · protein-protein
- G–H · 791 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 7LK4 · Crystal structure of BAK L100A in complex with activating antibody fragments · the same entry in another collection · chain H against H, 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 Q16611
- Elsewhere: RCSB PDB 7LK4 · PDBe 7LK4 · UniProt Q16611
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