Research workbench
Crystal structure of mouse bak BH3-in-groove homodimer (GFP)
Analyse Crystal structure of mouse bak BH3-in-groove homodimer (GFP) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KTG
- Type
- protein
- Length
- 616 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Green fluorescent protein, BCL-2 homologous ANTAGONIST/KILLER
- UniProt
- P42212, O08734
- Ligands
- CR2
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Green fluorescent protein, BCL-2 homologous ANTAGONIST/KILLER | protein | 308 | 30% helix, 38% strand | P42212, O08734 |
Ligands and binding sites
- CR2 · {(4Z)-2-(aminomethyl)-4-[(4-hydroxyphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 520 | 0.77 | 0.84 | 63 | empty |
| 2 | 95 | 0.75 | 0.96 | 23 | CR2 |
| 3 | 77 | 0.74 | 0.97 | 24 | CR2 |
| 4 | 117 | 0.46 | 0.79 | 26 | empty |
| 5 | 80 | 0.43 | 0.80 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1925 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 cofactor (chromophore).
Compared structures
- 5KTG · Crystal structure of mouse Bak BH3-in-groove homodimer (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 B against A, TM-score 0.75
- O08734 · AlphaFold monomer V2.0 prediction for BCL-2 homologous ANTAGONIST/KILLER (O08734) · a predicted model of the same protein · chain B against A, TM-score 0.26
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 O08734
- Elsewhere: RCSB PDB 5KTG · PDBe 5KTG · UniProt P42212 · UniProt O08734
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