Research workbench
Allosteric activation of human prekallikrein by apple domain disc rotation
Analyse Allosteric activation of human prekallikrein by apple domain disc rotation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6I44
- Type
- protein
- Length
- 594 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Plasma kallikrein
- EC
- 3.4.21.34
- UniProt
- P03952
- Ligands
- BEN, GLY, SER, NAG, NA, SO4, CL
- Pockets
- 7 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 15% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Plasma kallikrein (EC 3.4.21.34) | protein | 594 | 15% helix, 37% strand | P03952 |
Ligands and binding sites
- BEN · Benzamidine · ligand · chains A
- GLY · Glycine · ligand · chains A
- SER · Serine · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- NA · Sodium ion · metal · chains A
- SO4 · Sulfate ion · ion · chains A
- CL · Chloride ion · ion · chains A
- FMT · Formic acid · additive · 8 copies · chains A
- ACT · Acetate ion · additive · 6 copies · chains A
- GOL · Glycerol · additive · 4 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A
- PE4 · 2-{2-[2-(2-{2-[2-(2-ethoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethanol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 676 | 0.83 | 0.87 | 70 | MPD, SO4, FMT, ACT |
| 2 | 651 | 0.79 | 0.84 | 64 | FMT, ACT, GLY |
| 3 | 61 | 0.53 | 0.87 | 19 | empty |
| 4 | 169 | 0.48 | 0.76 | 35 | BEN, PEG |
| 5 | 56 | 0.35 | 0.78 | 14 | GOL |
Modifications
Observed in the structure: 18 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 6I44 · Allosteric activation of human prekallikrein by apple domain disc rotation · the same entry in another collection · chain A against A, TM-score 1.00
- P03952 · AlphaFold monomer V2.0 prediction for plasma kallikrein (P03952) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P03952
- Elsewhere: RCSB PDB 6I44 · PDBe 6I44 · UniProt P03952
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