MolNFT v1 · #118659 · protein
The crystal structure of human plasma kallikrein in complex with its peptide inhibitor pkalin-2
5F8T · Plasma kallikrein light chain: “The crystal structure of human plasma kallikrein in complex with its peptide inhibitor pkalin-2”. X-ray diffraction, 2 ligands (MRZ, SO4), 2 pockets (best druggability 0.45). MolNFT v1 #118659 on…
- PDB
- 5F8T
- Type
- protein
- Length
- 249 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Plasma kallikrein light chain; Cys-pro-lys-arg-phe-M70-ala-leu-phe-cys
- EC
- 3.4.21.34
- UniProt
- P03952
- Ligands
- MRZ, SO4
- Pockets
- 2 · best druggability 0.45
Structure
x-ray diffraction · 2 distinct chains · 14% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Plasma kallikrein light chain (EC 3.4.21.34) | protein | 239 | 15% helix, 35% strand | P03952 |
| P | Cys-pro-lys-arg-phe-M70-ala-leu-phe-cys | protein | 10 | 0% helix, 10% strand | — |
Ligands and binding sites
- MRZ · piperidine-1-carboximidamide · ligand · chains A, P
- SO4 · Sulfate ion · ion · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 59 | 0.45 | 0.83 | 17 | empty |
| 2 | 54 | 0.40 | 0.81 | 18 | empty |
Interfaces
1 interface between chains.
- A–P · 655 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 5F8T · The crystal structure of human Plasma Kallikrein in complex with its peptide inhibitor… · the same entry in another collection · chain A against A, TM-score 1.00
- 5F8T · The crystal structure of human Plasma Kallikrein in complex with its peptide inhibitor… · 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 0.98
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 P03952
- Elsewhere: RCSB PDB 5F8T · PDBe 5F8T · UniProt P03952
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