MolNFT v1 · #160208 · protein
Ancestral effector caspase 3/6/7
6PDQ · Ancestral effector caspase-3/6/7: “Ancestral effector caspase 3/6/7”. X-ray diffraction, 1 ligand (ACE), 1 pocket (best druggability 0.71). MolNFT v1 #160208 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6PDQ
- Type
- protein
- Length
- 461 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ancestral effector caspase-3/6/7; Ac-devd inhibitor
- Ligands
- ACE
- Pockets
- 1 · best druggability 0.71
Structure
x-ray diffraction · 5 distinct chains · 29% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ancestral effector caspase-3/6/7 | protein | 139 | 29% helix, 29% strand | — |
| B | Ancestral effector caspase-3/6/7 | protein | 87 | 30% helix, 22% strand | — |
| D | Ancestral effector caspase-3/6/7 | protein | 142 | 28% helix, 27% strand | — |
| E | Ancestral effector caspase-3/6/7 | protein | 85 | 31% helix, 22% strand | — |
| F, G | Ac-devd inhibitor | protein | 4 | 0% helix, 50% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains E, F, B, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 472 | 0.71 | 0.81 | 44 | empty |
Interfaces
10 interfaces between chains.
- A–B · 2168 Ų buried · 44 hydrogen bonds · protein-protein
- D–E · 2125 Ų buried · 39 hydrogen bonds · protein-protein
- B–E · 1209 Ų buried · 14 hydrogen bonds · protein-protein
- B–G · 383 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 380 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6PDQ · Ancestral Effector Caspase 3/6/7 · the same entry in another collection · chain G against G, 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
- Elsewhere: RCSB PDB 6PDQ · PDBe 6PDQ
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