MolNFT v1 · #60927 · protein
Crystal structure of human caspase-1 with a naturally-occurring ARG240->gln substitution in complex with 3-[2-(2- benzyloxycarbonylamino-3-methyl-butyrylamino)-propionylamino]-4-oxo- pentanoic acid (Z-vad-fmk)
3D6F: “Crystal structure of human caspase-1 with a naturally-occurring ARG240->gln substitution in complex with…”. X-ray diffraction, 2 ligands (PHQ, CF0), 1 pocket (best druggability 0.46). MolNFT v1 #60927 on GenesisL1: 3D structure…
- PDB
- 3D6F
- Type
- protein
- Length
- 264 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Caspase-1; 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 0.46
Structure
x-ray diffraction · 3 distinct chains · 29% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Caspase-1 (EC 3.4.22.36) | protein | 173 | 30% helix, 19% strand | P29466 |
| B | Caspase-1 (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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 59 | 0.46 | 0.84 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2698 Ų buried · 48 hydrogen bonds · protein-protein
- B–C · 225 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 167 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 3D6F · Crystal structure of human caspase-1 with a naturally-occurring Arg240->Gln substitution… · 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 3D6F · PDBe 3D6F · UniProt P29466
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.