Research workbench
Structural insights into the proteolytic machinery of apoptosis- inducing granzyme M
Analyse Structural insights into the proteolytic machinery of apoptosis- inducing… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ZKS
- Type
- protein
- Length
- 235 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Granzyme M; Hgzmm inhibitor
- EC
- 3.4.21.-
- UniProt
- P51124
- Ligands
- ACE, SO4, 0QE
- Pockets
- 3 · best druggability 0.39
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Granzyme M (EC 3.4.21.-) | protein | 231 | 10% helix, 36% strand | P51124 |
| C | Hgzmm inhibitor | protein | 4 | 0% helix, 50% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains A, C
- SO4 · Sulfate ion · ion · 4 copies · chains A
- 0QE · Chloromethane · ion · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 68 | 0.39 | 0.79 | 20 | empty |
| 2 | 99 | 0.36 | 0.74 | 21 | empty |
| 3 | 56 | 0.31 | 0.76 | 19 | empty |
Interfaces
1 interface between chains.
- A–C · 438 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 2ZKS · Structural insights into the proteolytic machinery of apoptosis-inducing Granzyme M · the same entry in another collection · chain A against A, TM-score 1.00
- P51124 · AlphaFold monomer V2.0 prediction for granzyme M (P51124) · a predicted model of the same protein · 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 P51124
- Elsewhere: RCSB PDB 2ZKS · PDBe 2ZKS · UniProt P51124
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