MolNFT v1 · #17301 · protein
Crystal structure of human granzyme a
1OP8: “Crystal structure of human granzyme a”. X-ray diffraction, 1 ligand (SO4), 16 pockets (best druggability 0.77). MolNFT v1 #17301 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1OP8
- Type
- protein
- Length
- 1,404 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Granzyme a
- EC
- 3.4.21.78
- UniProt
- P12544
- Ligands
- SO4
- Pockets
- 16 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 7% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Granzyme a (EC 3.4.21.78) | protein | 234 | 7% helix, 35% strand | P12544 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 12 copies · chains A, B, E, C, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 975 | 0.77 | 0.79 | 94 | SO4 |
| 2 | 119 | 0.67 | 0.90 | 34 | empty |
| 3 | 69 | 0.65 | 0.93 | 21 | empty |
| 4 | 51 | 0.61 | 0.93 | 16 | empty |
| 5 | 220 | 0.56 | 0.79 | 37 | empty |
Interfaces
7 interfaces between chains.
- C–D · 736 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 726 Ų buried · 5 hydrogen bonds · protein-protein
- E–F · 706 Ų buried · 7 hydrogen bonds · protein-protein
- D–E · 421 Ų buried · 3 hydrogen bonds · protein-protein
- B–E · 388 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 27 disulfide (disulfide).
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 P12544
- Elsewhere: RCSB PDB 1OP8 · PDBe 1OP8 · UniProt P12544
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