Research workbench
The oligomeric structure of human granzyme a reveals the molecular determinants of substrate specificity
Analyse The oligomeric structure of human granzyme a reveals the molecular determinants… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ORF
- Type
- protein
- Length
- 232 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Granzyme a
- EC
- 3.4.21.78
- UniProt
- P12544
- Ligands
- 0G6, SO4
- Pockets
- 1 · best druggability 0.47
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Granzyme a (EC 3.4.21.78) | protein | 232 | 6% helix, 33% strand | P12544 |
Ligands and binding sites
- 0G6 · D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide · ligand · chains A
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 158 | 0.47 | 0.77 | 32 | 0G6 |
Modifications
Observed in the structure: 4 disulfide, 2 covalent (disulfide, covalent ligand).
Compared structures
- 1ORF · The Oligomeric Structure of Human Granzyme A Reveals the Molecular Determinants of… · the same entry in another collection · chain A against A, TM-score 1.00
- P12544 · AlphaFold monomer V2.0 prediction for granzyme a (P12544) · 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 P12544
- Elsewhere: RCSB PDB 1ORF · PDBe 1ORF · UniProt P12544
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