MolNFT v1 · #18745 · protein
Crystal structure of human caspase-2 in complex with acetyl-leu-asp- glu-ser-asp-cho
1PYO: “Crystal structure of human caspase-2 in complex with acetyl-leu-asp- glu-ser-asp-cho”. X-ray diffraction, 1 ligand (ACE), 6 pockets (best druggability 0.79). MolNFT v1 #18745 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1PYO
- Type
- protein
- Length
- 527 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Caspase-2; Acetyl-leu-asp-glu-ser-asj
- EC
- 3.4.22.-
- UniProt
- P42575, P36114
- Ligands
- ACE
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 5 distinct chains · 30% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Caspase-2 (EC 3.4.22.-) | protein | 159 | 31% helix, 25% strand | P42575 |
| B | Caspase-2 (EC 3.4.22.-) | protein | 98 | 27% helix, 19% strand | P42575 |
| E, F | Acetyl-leu-asp-glu-ser-asj | protein | 5 | 0% helix, 60% strand | P36114 |
| C | Caspase-2 (EC 3.4.22.-) | protein | 161 | 32% helix, 25% strand | P42575 |
| D | Caspase-2 (EC 3.4.22.-) | protein | 99 | 27% helix, 19% strand | P42575 |
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
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 494 | 0.79 | 0.86 | 64 | empty |
| 2 | 106 | 0.41 | 0.77 | 17 | empty |
| 3 | 127 | 0.38 | 0.74 | 22 | empty |
| 4 | 99 | 0.33 | 0.73 | 19 | empty |
| 5 | 71 | 0.32 | 0.75 | 19 | empty |
Interfaces
10 interfaces between chains.
- A–B · 2711 Ų buried · 46 hydrogen bonds · protein-protein
- C–D · 2675 Ų buried · 41 hydrogen bonds · protein-protein
- B–D · 1431 Ų buried · 21 hydrogen bonds · protein-protein
- D–F · 488 Ų buried · 15 hydrogen bonds · protein-protein
- B–E · 486 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 modified, 1 disulfide (covalent ligand, nonstandard, disulfide).
Compared structures
- 1PYO · Crystal Structure of Human Caspase-2 in Complex with Acetyl-Leu-Asp-Glu-Ser-Asp-cho · the same entry in another collection · chain F against F, TM-score 1.00
- P42575 · AlphaFold monomer V2.0 prediction for caspase-2 (P42575) · a predicted model of the same protein · chain C against A, TM-score 0.99
- P36114 · AlphaFold monomer V2.0 prediction for IML2-like protein YKR018C (P36114) · a predicted model of the same protein · chain E against A, TM-score 0.65
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
- Every structure of UniProt P36114
- Elsewhere: RCSB PDB 1PYO · PDBe 1PYO · UniProt P42575 · UniProt P36114
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