Research workbench
Crystal structure of hybcl-2-4 with HYBAK1 BH3
Analyse Crystal structure of hybcl-2-4 with HYBAK1 BH3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WGZ
- Type
- protein
- Length
- 538 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Maltodextrin-binding protein; BCL-2-like 4; Bak
- UniProt
- A0A4Z0THX4, A7LM80, A1E3K5
- Ligands
- GLC
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 55% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Maltodextrin-binding protein | protein | 365 | 46% helix, 19% strand | A0A4Z0THX4 |
| B | BCL-2-like 4 | protein | 151 | 73% helix, 0% strand | A7LM80 |
| C | Bak | protein | 22 | 82% helix, 0% strand | A1E3K5 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 3 copies · chains A
- ACT · Acetate ion · additive · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 349 | 0.75 | 0.86 | 33 | GLC |
| 2 | 239 | 0.67 | 0.84 | 30 | empty |
| 3 | 293 | 0.52 | 0.75 | 40 | empty |
| 4 | 97 | 0.41 | 0.78 | 16 | empty |
| 5 | 63 | 0.29 | 0.74 | 17 | empty |
Interfaces
2 interfaces between chains.
- B–C · 958 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 346 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6WGZ · Crystal structure of HyBcl-2-4 with HyBak1 BH3 · 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 A0A4Z0THX4
- Every structure of UniProt A7LM80
- Every structure of UniProt A1E3K5
- Elsewhere: RCSB PDB 6WGZ · PDBe 6WGZ · UniProt A0A4Z0THX4 · UniProt A7LM80 · UniProt A1E3K5
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