MolNFT v1 · #164009 · protein
Crystal structure of human kallikrein 6 (I218Y) in complex with GSK3448330A
6SKC · Kallikrein-6: “Crystal structure of human kallikrein 6 (I218Y) in complex with GSK3448330A”. X-ray diffraction, 2 ligands (LH8, BEN), 4 pockets (best druggability 0.69). MolNFT v1 #164009 on GenesisL1: 3D structure, binding sites…
- PDB
- 6SKC
- Type
- protein
- Length
- 444 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kallikrein-6
- EC
- 3.4.21.-
- UniProt
- Q92876
- Ligands
- LH8, BEN
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 10% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Kallikrein-6 (EC 3.4.21.-) | protein | 222 | 10% helix, 39% strand | Q92876 |
Ligands and binding sites
- LH8 · 4-[(3~{S})-1-oxidanyl-3,4-dihydro-2,1-benzoxaborinin-3-yl]benzenecarboximidamide · ligand · chains A
- BEN · Benzamidine · ligand · chains B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 600 | 0.69 | 0.78 | 55 | BEN |
| 2 | 63 | 0.53 | 0.87 | 24 | empty |
| 3 | 74 | 0.41 | 0.80 | 17 | LH8 |
| 4 | 74 | 0.33 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 562 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
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 Q92876
- Elsewhere: RCSB PDB 6SKC · PDBe 6SKC · UniProt Q92876
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