Research workbench
Crystal structure of the inhibitor-free form of the serine protease kallikrein-4
Analyse Crystal structure of the inhibitor-free form of the serine protease kallikrein-4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NVB
- Type
- protein
- Length
- 894 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kallikrein-4
- EC
- 3.4.21.-
- UniProt
- Q9Y5K2
- Ligands
- SO4
- Pockets
- 12 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Kallikrein-4 (EC 3.4.21.-) | protein | 223 | 11% helix, 37% strand | Q9Y5K2 |
| B, D | Kallikrein-4 (EC 3.4.21.-) | protein | 224 | 12% helix, 38% strand | Q9Y5K2 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains B, D
- GOL · Glycerol · additive · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 460 | 0.61 | 0.76 | 44 | GOL |
| 2 | 205 | 0.52 | 0.77 | 30 | empty |
| 3 | 78 | 0.50 | 0.85 | 22 | GOL, SO4 |
| 4 | 75 | 0.50 | 0.85 | 21 | GOL, SO4 |
| 5 | 83 | 0.49 | 0.83 | 22 | GOL |
Interfaces
3 interfaces between chains.
- A–D · 484 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 380 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 374 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide (disulfide).
Compared structures
- 6NVB · Crystal structure of the inhibitor-free form of the serine protease kallikrein-4 · the same entry in another collection · chain D against D, TM-score 1.00
- Q9Y5K2 · AlphaFold monomer V2.0 prediction for kallikrein-4 (Q9Y5K2) · a predicted model of the same protein · chain A against A, 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 Q9Y5K2
- Elsewhere: RCSB PDB 6NVB · PDBe 6NVB · UniProt Q9Y5K2
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