Research workbench
Structural insight into zymogenic latency of gingipain K from porphyromonas gingivalis.
Analyse Structural insight into zymogenic latency of gingipain K from porphyromonas… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MUN
- Type
- protein
- Length
- 359 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lys-gingipain W83
- EC
- 3.4.22.47
- UniProt
- Q51817
- Ligands
- AZI
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 3% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lys-gingipain W83 (EC 3.4.22.47) | protein | 182 | 3% helix, 58% strand | Q51817 |
| B | Lys-gingipain W83 (EC 3.4.22.47) | protein | 177 | 2% helix, 57% strand | Q51817 |
Ligands and binding sites
- AZI · Azide ion · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 330 | 0.73 | 0.85 | 41 | AZI |
| 2 | 234 | 0.68 | 0.84 | 31 | empty |
| 3 | 71 | 0.55 | 0.87 | 19 | empty |
| 4 | 168 | 0.50 | 0.78 | 30 | empty |
| 5 | 59 | 0.26 | 0.73 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1089 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 5MUN · Structural insight into zymogenic latency of gingipain K from Porphyromonas gingivalis. · the same entry in another collection · chain A against A, TM-score 1.00
- Q51817 · AlphaFold monomer V2.0 prediction for lys-gingipain W83 (Q51817) · a predicted model of the same protein · chain B against A, TM-score 0.94
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 Q51817
- Elsewhere: RCSB PDB 5MUN · PDBe 5MUN · UniProt Q51817
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