MolNFT v1 · #164008 · protein
Crystal structure of human kallikrein 6 (N217D/I218Y/K224R) in complex with GSK3496783A
6SKB · Kallikrein-6: “Crystal structure of human kallikrein 6 (N217D/I218Y/K224R) in complex with GSK3496783A”. X-ray diffraction, 2 ligands (LH5, RH5), 7 pockets (best druggability 0.71). MolNFT v1 #164008 on GenesisL1: 3D structure…
- PDB
- 6SKB
- Type
- protein
- Length
- 667 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kallikrein-6
- EC
- 3.4.21.-
- UniProt
- Q92876
- Ligands
- LH5, RH5
- Pockets
- 7 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Kallikrein-6 (EC 3.4.21.-) | protein | 223 | 10% helix, 39% strand | Q92876 |
| B, C | Kallikrein-6 (EC 3.4.21.-) | protein | 222 | 10% helix, 38% strand | Q92876 |
Ligands and binding sites
- LH5 · 4-[(3~{S})-1-oxidanyl-3,4-dihydro-2,1-benzoxaborinin-3-yl]-2-(pyridin-3-ylmethoxy)benzenecarboximidamide · ligand · 3 copies · chains A, B, C
- RH5 · 4-[(3~{R})-1-oxidanyl-3,4-dihydro-2,1-benzoxaborinin-3-yl]-2-(pyridin-3-ylmethoxy)benzenecarboximidamide · ligand · 3 copies · chains A, B, C
- GOL · Glycerol · additive · chains C
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 | 556 | 0.71 | 0.80 | 51 | RH5, LH5 |
| 2 | 354 | 0.63 | 0.78 | 41 | empty |
| 3 | 439 | 0.61 | 0.76 | 55 | empty |
| 4 | 103 | 0.41 | 0.77 | 21 | LH5, RH5 |
| 5 | 84 | 0.38 | 0.77 | 18 | LH5, RH5 |
Interfaces
3 interfaces between chains.
- A–C · 586 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 475 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 11 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 6 covalent (disulfide, covalent ligand).
Compared structures
- 6SKB · Crystal Structure of Human Kallikrein 6 (N217D/I218Y/K224R) in complex with GSK3496783A · the same entry in another collection · chain A against A, TM-score 1.00
- Q92876 · AlphaFold monomer V2.0 prediction for kallikrein-6 (Q92876) · a predicted model of the same protein · chain B 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 Q92876
- Elsewhere: RCSB PDB 6SKB · PDBe 6SKB · UniProt Q92876
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