MolNFT v1 · #38630 · protein
Crystal structure of human caspase-1 (CYS362->ala, CYS364->ala, CYS397->ala) in complex with 3-[2-(2-benzyloxycarbonylamino-3-methyl- butyrylamino)-propionylamino]-4-oxo-pentanoic acid (Z-vad-fmk)
2H48 · Caspase 1, isoform gamma: “Crystal structure of human caspase-1 (CYS362->ala, CYS364->ala, CYS397->ala) in complex with…”. X-ray diffraction, 2 ligands (PHQ, CF0), 1 pocket (best druggability 0.50). MolNFT v1 #38630 on GenesisL1: 3D…
- PDB
- 2H48
- Type
- protein
- Length
- 264 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Caspase 1, isoform gamma; N-[(BENZYLOXY)CARBONYL]-L-valyl-N-[(2S)-1-carboxy-4-fluoro…
- EC
- 3.4.22.36
- UniProt
- P29466
- Ligands
- PHQ, CF0
- Pockets
- 1 · best druggability 0.50
Structure
x-ray diffraction · 3 distinct chains · 29% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Caspase 1, isoform gamma (EC 3.4.22.36) | protein | 173 | 30% helix, 18% strand | P29466 |
| B | Caspase 1, isoform gamma (EC 3.4.22.36) | protein | 88 | 27% helix, 17% strand | P29466 |
| C | N-[(BENZYLOXY)CARBONYL]-L-valyl-N-[(2S)-1-carboxy-4-fluoro- 3-oxobutan-2-yl]-L-alaninamide | protein | 3 | 0% helix, 33% strand | — |
Ligands and binding sites
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 | 67 | 0.50 | 0.85 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2734 Ų buried · 47 hydrogen bonds · protein-protein
- B–C · 229 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 169 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 2H48 · Crystal structure of human caspase-1 (Cys362->Ala, Cys364->Ala, Cys397->Ala) in complex… · the same entry in another collection · chain A against A, TM-score 1.00
- P29466 · AlphaFold monomer V2.0 prediction for caspase-1 (P29466) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 P29466
- Elsewhere: RCSB PDB 2H48 · PDBe 2H48 · UniProt P29466
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