MolNFT v1 · #144009 · protein
Caspase-3 mutant- D9A,D28A,T152D
6BGK: “Caspase-3 mutant- D9A,D28A,T152D”. X-ray diffraction, 5 ligands (ACE, NA, CL), 3 pockets (best druggability 0.65). MolNFT v1 #144009 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6BGK
- Type
- protein
- Length
- 487 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Caspase-3; ACE-asp-glu-val-asp-0QE
- EC
- 3.4.22.56
- UniProt
- P42574
- Ligands
- ACE, NA, CL, 0QE, AZI
- Pockets
- 3 · best druggability 0.65
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Caspase-3 (EC 3.4.22.56) | protein | 146 | 26% helix, 31% strand | P42574 |
| C | Caspase-3 (EC 3.4.22.56) | protein | 94 | 33% helix, 20% strand | P42574 |
| D | Caspase-3 (EC 3.4.22.56) | protein | 93 | 33% helix, 20% strand | P42574 |
| F, H | ACE-asp-glu-val-asp-0QE | protein | 4 | 0% helix, 50% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains C, F, D, H
- NA · Sodium ion · metal · 3 copies · chains B, D
- CL · Chloride ion · ion · 4 copies · chains A, C, B, D
- 0QE · Chloromethane · ion · 2 copies · chains A, F, B, H
- AZI · Azide ion · ion · 2 copies · chains C, B, D, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 310 | 0.65 | 0.81 | 39 | empty |
| 2 | 85 | 0.36 | 0.75 | 20 | empty |
| 3 | 51 | 0.32 | 0.77 | 15 | empty |
Interfaces
10 interfaces between chains.
- A–C · 2257 Ų buried · 37 hydrogen bonds · protein-protein
- B–D · 2247 Ų buried · 36 hydrogen bonds · protein-protein
- C–D · 1460 Ų buried · 20 hydrogen bonds · protein-protein
- C–B · 475 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 461 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
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 P42574
- Elsewhere: RCSB PDB 6BGK · PDBe 6BGK · UniProt P42574
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