Research workbench
Crystal structure of active human granzyme H
Analyse Crystal structure of active human granzyme H in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GAW
- Type
- protein
- Length
- 2,705 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Granzyme H
- EC
- 3.4.21.-
- UniProt
- P20718
- Ligands
- SO4, CL
- Pockets
- 20 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Granzyme H (EC 3.4.21.-) | protein | 224 | 6% helix, 28% strand | P20718 |
| B, C, D, E, F, G, I, J, K, L | Granzyme H (EC 3.4.21.-) | protein | 226 | 8% helix, 35% strand | P20718 |
| H | Granzyme H (EC 3.4.21.-) | protein | 221 | 10% helix, 36% strand | P20718 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 15 copies · chains B, G, D, H, E, F, I, J, L
- CL · Chloride ion · ion · 3 copies · chains C, D, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 440 | 0.69 | 0.81 | 62 | SO4 |
| 2 | 469 | 0.67 | 0.79 | 55 | SO4 |
| 3 | 425 | 0.65 | 0.78 | 58 | SO4 |
| 4 | 399 | 0.63 | 0.78 | 57 | SO4 |
| 5 | 385 | 0.63 | 0.78 | 54 | empty |
Interfaces
12 interfaces between chains.
- A–K · 868 Ų buried · 8 hydrogen bonds · protein-protein
- D–H · 865 Ų buried · 9 hydrogen bonds · protein-protein
- J–L · 828 Ų buried · 8 hydrogen bonds · protein-protein
- B–G · 800 Ų buried · 10 hydrogen bonds · protein-protein
- C–K · 783 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 disulfide (disulfide).
Compared structures
- 4GAW · Crystal structure of active human granzyme H · the same entry in another collection · chain L against L, 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 P20718
- Elsewhere: RCSB PDB 4GAW · PDBe 4GAW · UniProt P20718
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