Research workbench
Catalytic domain of human calpain 8
Analyse Catalytic domain of human calpain 8 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2NQA
- Type
- protein
- Length
- 634 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Calpain-8; Leupeptin inhibitor
- EC
- 3.4.22.53
- UniProt
- A6NHC0
- Ligands
- ACE, CA
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Calpain-8 (EC 3.4.22.53) | protein | 310 | 30% helix, 24% strand | A6NHC0 |
| B | Calpain-8 (EC 3.4.22.53) | protein | 318 | 29% helix, 23% strand | A6NHC0 |
| D, E | Leupeptin inhibitor | protein | 3 | 0% helix, 33% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains A, B, D, E
- CA · Calcium ion · metal · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 330 | 0.83 | 0.93 | 71 | empty |
| 2 | 283 | 0.67 | 0.83 | 48 | ACE |
| 3 | 136 | 0.65 | 0.87 | 27 | empty |
| 4 | 133 | 0.61 | 0.86 | 31 | empty |
| 5 | 182 | 0.52 | 0.78 | 29 | ACE |
Interfaces
5 interfaces between chains.
- A–B · 1131 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 359 Ų buried · 9 hydrogen bonds · protein-protein
- B–E · 342 Ų buried · 5 hydrogen bonds · protein-protein
- A–E · 115 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 110 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified, 2 covalent (oxidation, covalent ligand, nonstandard).
Compared structures
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 A6NHC0
- Elsewhere: RCSB PDB 2NQA · PDBe 2NQA · UniProt A6NHC0
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