Research workbench
Crystal structure of metacaspase 4 from arabidopsis (microcrystals treated with calcium)
Analyse Crystal structure of metacaspase 4 from arabidopsis (microcrystals treated with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6W8T
- Type
- protein
- Length
- 693 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Metacaspase-4
- EC
- 3.4.22.-
- UniProt
- O64517
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Metacaspase-4 (EC 3.4.22.-) | protein | 358 | 35% helix, 18% strand | O64517 |
| B | Metacaspase-4 (EC 3.4.22.-) | protein | 335 | 39% helix, 16% strand | O64517 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 580 | 0.70 | 0.79 | 59 | empty |
| 2 | 290 | 0.63 | 0.80 | 40 | empty |
| 3 | 50 | 0.41 | 0.82 | 11 | empty |
| 4 | 78 | 0.37 | 0.77 | 28 | empty |
| 5 | 63 | 0.30 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 699 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6W8T · Crystal structure of metacaspase 4 from Arabidopsis (microcrystals treated with calcium) · the same entry in another collection · chain A against A, TM-score 1.00
- O64517 · AlphaFold monomer V2.0 prediction for metacaspase-4 (O64517) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 O64517
- Elsewhere: RCSB PDB 6W8T · PDBe 6W8T · UniProt O64517
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