Research workbench
Human kallikrein 7 with aromatic coumarinic ester compound 3 covalently bound to H57
Analyse Human kallikrein 7 with aromatic coumarinic ester compound 3 covalently bound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SJU
- Type
- protein
- Length
- 1,792 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kallikrein-7
- EC
- 3.4.21.117
- UniProt
- P49862
- Ligands
- LFW, SO4
- Pockets
- 12 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 12% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Kallikrein-7 (EC 3.4.21.117) | protein | 224 | 12% helix, 37% strand | P49862 |
Ligands and binding sites
- LFW · (3-iodanylphenyl) 6-methyl-2-oxidanylidene-chromene-3-carboxylate · ligand · 8 copies · chains A, B, C, E, D, H, F, G
- SO4 · Sulfate ion · ion · 90 copies · chains A, D, B, H, C, E, G, F
- PGE · Triethylene glycol · additive · 6 copies · chains A, C, D, H, B, E, F
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains A, H, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 983 | 0.88 | 0.89 | 114 | SO4, LFW |
| 2 | 733 | 0.87 | 0.91 | 101 | PGE, LFW |
| 3 | 749 | 0.87 | 0.90 | 110 | SO4, LFW |
| 4 | 901 | 0.86 | 0.88 | 98 | PGE, SO4 |
| 5 | 867 | 0.83 | 0.85 | 89 | PGE, SO4, EPE |
Interfaces
13 interfaces between chains.
- D–H · 1011 Ų buried · 8 hydrogen bonds · protein-protein
- C–E · 988 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 986 Ų buried · 9 hydrogen bonds · protein-protein
- C–G · 480 Ų buried · 10 hydrogen bonds · protein-protein
- D–F · 435 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 disulfide, 8 covalent (disulfide, covalent ligand).
Compared structures
- 6SJU · Human kallikrein 7 with aromatic coumarinic ester compound 3 covalently bound to H57 · the same entry in another collection · chain H against H, TM-score 1.00
- P49862 · AlphaFold monomer V2.0 prediction for kallikrein-7 (P49862) · a predicted model of the same protein · chain A 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 P49862
- Elsewhere: RCSB PDB 6SJU · PDBe 6SJU · UniProt P49862
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