Research workbench
Caspase-2 bound to one copy of ac-dvad-cho
Analyse Caspase-2 bound to one copy of ac-dvad-cho in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3R7B
- Type
- protein
- Length
- 510 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Caspase-2 subunit P18; Caspase-2 subunit P12; Peptide inhibitor (ACE)DVAD-cho
- EC
- 3.4.22.55
- UniProt
- P42575
- Ligands
- ACE
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 5 distinct chains · 30% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Caspase-2 subunit P18 (EC 3.4.22.55) | protein | 156 | 32% helix, 24% strand | P42575 |
| B | Caspase-2 subunit P12 (EC 3.4.22.55) | protein | 95 | 28% helix, 18% strand | P42575 |
| C | Caspase-2 subunit P18 (EC 3.4.22.55) | protein | 159 | 31% helix, 25% strand | P42575 |
| D | Caspase-2 subunit P12 (EC 3.4.22.55) | protein | 96 | 28% helix, 20% strand | P42575 |
| F | Peptide inhibitor (ACE)DVAD-cho | protein | 4 | 0% helix, 50% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 386 | 0.78 | 0.88 | 58 | empty |
| 2 | 115 | 0.39 | 0.75 | 24 | empty |
| 3 | 115 | 0.39 | 0.74 | 23 | empty |
| 4 | 82 | 0.38 | 0.77 | 20 | empty |
| 5 | 50 | 0.29 | 0.76 | 12 | empty |
Interfaces
8 interfaces between chains.
- C–D · 2628 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 2541 Ų buried · 38 hydrogen bonds · protein-protein
- B–D · 1346 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 412 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 409 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent, 1 disulfide, 1 modified (covalent ligand, disulfide, 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 P42575
- Elsewhere: RCSB PDB 3R7B · PDBe 3R7B · UniProt P42575
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.