Research workbench
Crystal structure analysis of the K2 cleaved adhesin domain of lys- gingipain (kgp)
Analyse Crystal structure analysis of the K2 cleaved adhesin domain of lys- gingipain… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KM5
- Type
- protein
- Length
- 352 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine specific cysteine protease
- UniProt
- O52050
- Ligands
- CA, NO3, SO4
- Pockets
- 2 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 2% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine specific cysteine protease | protein | 179 | 2% helix, 38% strand | O52050 |
| B | Lysine specific cysteine protease | protein | 173 | 2% helix, 40% strand | O52050 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B
- NO3 · Nitrate ion · ion · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A, B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 178 | 0.55 | 0.80 | 33 | SO4 |
| 2 | 90 | 0.33 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 379 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3KM5 · Crystal Structure Analysis of the K2 Cleaved Adhesin Domain of Lys-gingipain (Kgp) · the same entry in another collection · 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 O52050
- Elsewhere: RCSB PDB 3KM5 · PDBe 3KM5 · UniProt O52050
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