MolNFT v1 · #21274 · protein
The 2.0 a crystal structure of the kdel-tailed cysteine endopeptidase functioning in programmed cell death of ricinus communis endosperm
1S4V: “The 2.0 a crystal structure of the kdel-tailed cysteine endopeptidase functioning in programmed cell death of…”. X-ray diffraction, 2 ligands (0QE, SO4), 1 pocket (best druggability 0.55). MolNFT v1 #21274 on GenesisL1: 3D…
- PDB
- 1S4V
- Type
- protein
- Length
- 456 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cysteine endopeptidase; Dva-leu-lys-0QE peptide
- Ligands
- 0QE, SO4
- Pockets
- 1 · best druggability 0.55
Structure
x-ray diffraction · 3 distinct chains · 25% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cysteine endopeptidase | protein | 224 | 25% helix, 21% strand | — |
| B | Cysteine endopeptidase | protein | 226 | 25% helix, 21% strand | — |
| C, D | Dva-leu-lys-0QE peptide | 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 | 366 | 0.55 | 0.74 | 42 | empty |
Interfaces
4 interfaces between chains.
- B–D · 312 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 309 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 230 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 43 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 d-amino (disulfide, D-amino acid).
Compared structures
- 1S4V · The 2.0 A crystal structure of the KDEL-tailed cysteine endopeptidase functioning in… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 1S4V · PDBe 1S4V
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.