MolNFT v1 · #49354 · protein
Crystal structure of caspase-7 with inhibitor ac-wehd-cho
2QLJ: “Crystal structure of caspase-7 with inhibitor ac-wehd-cho”. X-ray diffraction, 1 ligand (ACE), 1 pocket (best druggability 0.75). MolNFT v1 #49354 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2QLJ
- Type
- protein
- Length
- 478 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Caspase-7; Inhibitor ac-wehd-cho; Peptide qghge
- EC
- 3.4.22.60
- UniProt
- P55210
- Ligands
- ACE
- Pockets
- 1 · best druggability 0.75
Structure
x-ray diffraction · 5 distinct chains · 30% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Caspase-7 (EC 3.4.22.60) | protein | 140 | 32% helix, 29% strand | P55210 |
| B | Caspase-7 (EC 3.4.22.60) | protein | 92 | 29% helix, 18% strand | P55210 |
| D | Caspase-7 (EC 3.4.22.60) | protein | 93 | 30% helix, 22% strand | P55210 |
| E, F | Inhibitor ac-wehd-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
- CIT · Citric acid · additive · chains A, B, C, D
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 | 538 | 0.75 | 0.82 | 40 | CIT |
Interfaces
14 interfaces between chains.
- A–B · 2300 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 2261 Ų buried · 33 hydrogen bonds · protein-protein
- B–D · 1448 Ų buried · 19 hydrogen bonds · protein-protein
- D–F · 477 Ų buried · 10 hydrogen bonds · protein-protein
- B–E · 452 Ų buried · 11 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 2QLJ · PDBe 2QLJ · UniProt P55210
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