MolNFT v1 · #49350 · protein
Crystal structure of caspase-7 with inhibitor ac-dnld-cho
2QLF: “Crystal structure of caspase-7 with inhibitor ac-dnld-cho”. X-ray diffraction, 1 ligand (ACE), 1 pocket (best druggability 0.77). MolNFT v1 #49350 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2QLF
- Type
- protein
- Length
- 477 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Caspase-7; Inhibitor ac-dnld-cho; Peptide qghge
- EC
- 3.4.22.60
- UniProt
- P55210
- Ligands
- ACE
- Pockets
- 1 · best druggability 0.77
Structure
x-ray diffraction · 6 distinct chains · 30% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Caspase-7 (EC 3.4.22.60) | protein | 139 | 28% helix, 34% strand | P55210 |
| B | Caspase-7 (EC 3.4.22.60) | protein | 92 | 33% helix, 21% strand | P55210 |
| C | Caspase-7 (EC 3.4.22.60) | protein | 140 | 29% helix, 30% strand | P55210 |
| D | Caspase-7 (EC 3.4.22.60) | protein | 93 | 33% helix, 20% strand | P55210 |
| E, F | Inhibitor ac-dnld-cho | protein | 4 | 0% helix, 50% strand | — |
| G | Peptide qghge | protein | 5 | 0% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains B, E, D, F
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 | 506 | 0.77 | 0.84 | 43 | empty |
Interfaces
14 interfaces between chains.
- A–B · 2301 Ų buried · 38 hydrogen bonds · protein-protein
- C–D · 2292 Ų buried · 37 hydrogen bonds · protein-protein
- B–D · 1434 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 436 Ų buried · 8 hydrogen bonds · protein-protein
- B–E · 422 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 modified (covalent ligand, nonstandard).
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 P55210
- Elsewhere: RCSB PDB 2QLF · PDBe 2QLF · UniProt P55210
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