Research workbench
Zebrafish caspase N213T
Analyse Zebrafish caspase N213T in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7JL7
- Type
- protein
- Length
- 476 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Caspase 3, apoptosis-related cysteine protease a; Asp-glu-val-asp peptide
- UniProt
- Q98UI8
- Pockets
- 3 · best druggability 0.70
Structure
x-ray diffraction · 5 distinct chains · 30% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Caspase 3, apoptosis-related cysteine protease a | protein | 141 | 28% helix, 30% strand | Q98UI8 |
| C | Caspase 3, apoptosis-related cysteine protease a | protein | 96 | 29% helix, 20% strand | Q98UI8 |
| B | Caspase 3, apoptosis-related cysteine protease a | protein | 141 | 30% helix, 30% strand | Q98UI8 |
| D | Caspase 3, apoptosis-related cysteine protease a | protein | 94 | 33% helix, 19% strand | Q98UI8 |
| F | Asp-glu-val-asp peptide | protein | 4 | 0% helix, 50% strand | — |
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 487 | 0.70 | 0.80 | 46 | empty |
| 2 | 86 | 0.39 | 0.77 | 21 | empty |
| 3 | 63 | 0.28 | 0.73 | 20 | empty |
Interfaces
8 interfaces between chains.
- B–D · 2265 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 2229 Ų buried · 35 hydrogen bonds · protein-protein
- C–D · 1334 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 454 Ų buried · 9 hydrogen bonds · protein-protein
- C–B · 418 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 7JL7 · Zebrafish Caspase N213T · 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
- Every structure of UniProt Q98UI8
- Elsewhere: RCSB PDB 7JL7 · PDBe 7JL7 · UniProt Q98UI8
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