MolNFT v1 · #112782 · protein
Caspase-7 variant 2 (V2) with reprogrammed substrate specificity due to Y230V/W232M/Q276C substitutions bound to veid inhibitor.
4ZVQ: “Caspase-7 variant 2 (V2) with reprogrammed substrate specificity due to Y230V/W232M/Q276C substitutions bound…”. X-ray diffraction, 1 ligand (ACE), 1 pocket (best druggability 0.77). MolNFT v1 #112782 on GenesisL1: 3D structure…
- PDB
- 4ZVQ
- Type
- protein
- Length
- 473 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Caspase-7; Peptide ACE-val-glu-ile-asa
- EC
- 3.4.22.60
- UniProt
- P55210
- Ligands
- ACE
- Pockets
- 1 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Caspase-7 (EC 3.4.22.60) | protein | 139 | 30% helix, 34% strand | P55210 |
| B, D | Caspase-7 (EC 3.4.22.60) | protein | 93 | 33% helix, 20% strand | P55210 |
| C | Caspase-7 (EC 3.4.22.60) | protein | 140 | 30% helix, 34% strand | P55210 |
| E, F | Peptide ACE-val-glu-ile-asa | protein | 4 | 0% helix, 50% 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 | 486 | 0.77 | 0.84 | 42 | empty |
Interfaces
10 interfaces between chains.
- C–D · 2291 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 2269 Ų buried · 36 hydrogen bonds · protein-protein
- B–D · 1422 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 443 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 435 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 modified (covalent ligand, nonstandard).
Compared structures
- 4ZVQ · Caspase-7 Variant 2 (V2) with reprogrammed substrate specificity due to Y230V/W232M/Q276C… · the same entry in another collection · chain F against F, TM-score 1.00
- P55210 · AlphaFold monomer V2.0 prediction for caspase-7 (P55210) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 4ZVQ · PDBe 4ZVQ · UniProt P55210
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