MolNFT v1 · #120300 · protein
Crystal structures of the serine protease domain of murine plasma kallikrein
5GVT: “Crystal structures of the serine protease domain of murine plasma kallikrein”. X-ray diffraction, 2 ligands (BMA, MAN), 7 pockets (best druggability 0.67). MolNFT v1 #120300 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5GVT
- Type
- protein
- Length
- 461 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Plasma kallikrein
- EC
- 3.4.21.34
- UniProt
- P26262
- Ligands
- BMA, MAN
- Pockets
- 7 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Plasma kallikrein (EC 3.4.21.34) | protein | 236 | 13% helix, 33% strand | P26262 |
| B | Plasma kallikrein (EC 3.4.21.34) | protein | 225 | 11% helix, 35% strand | P26262 |
Ligands and binding sites
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 301 | 0.67 | 0.82 | 37 | empty |
| 2 | 450 | 0.61 | 0.76 | 51 | empty |
| 3 | 125 | 0.48 | 0.79 | 21 | empty |
| 4 | 137 | 0.40 | 0.74 | 26 | empty |
| 5 | 83 | 0.37 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 561 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 5GVT · Crystal structures of the serine protease domain of murine plasma kallikrein · the same entry in another collection · chain A against A, TM-score 1.00
- P26262 · AlphaFold monomer V2.0 prediction for plasma kallikrein (P26262) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P26262
- Elsewhere: RCSB PDB 5GVT · PDBe 5GVT · UniProt P26262
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