Research workbench
Bax BH3-in-groove dimer (GFP)
Analyse Bax BH3-in-groove dimer (GFP) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BDU
- Type
- protein
- Length
- 1,180 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Green fluorescent protein, apoptosis regulator bax
- UniProt
- P42212, Q07812
- Ligands
- CR2
- Pockets
- 12 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 23% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Green fluorescent protein, apoptosis regulator bax | protein | 295 | 23% helix, 39% strand | P42212, Q07812 |
Ligands and binding sites
- CR2 · {(4Z)-2-(aminomethyl)-4-[(4-hydroxyphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 74 | 0.73 | 0.97 | 25 | CR2 |
| 2 | 73 | 0.73 | 0.97 | 24 | CR2 |
| 3 | 68 | 0.72 | 0.97 | 22 | CR2 |
| 4 | 66 | 0.70 | 0.96 | 20 | CR2 |
| 5 | 323 | 0.54 | 0.74 | 31 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2223 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 2218 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 106 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 102 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 32 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 cofactor (chromophore).
Compared structures
- 4BDU · Bax BH3-in-Groove dimer (GFP) · the same entry in another collection · chain A against A, TM-score 1.00
- P42212 · AlphaFold monomer V2.0 prediction for green fluorescent protein (P42212) · a predicted model of the same protein · chain C against A, TM-score 0.76
- Q07812 · AlphaFold monomer V2.0 prediction for apoptosis regulator bax (Q07812) · a predicted model of the same protein · chain B against A, TM-score 0.27
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 P42212
- Every structure of UniProt Q07812
- Elsewhere: RCSB PDB 4BDU · PDBe 4BDU · UniProt P42212 · UniProt Q07812
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