Research workbench
Matrix-metallopeptidase inhibitor Potempin A (PotA) from Tannerella forsythia in complex with T. forsythia karilysin.
Analyse Matrix-metallopeptidase inhibitor Potempin A (PotA) from Tannerella forsythia… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8B2Q
- Type
- protein
- Length
- 260 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.35
- Source
- Tannerella forsythia
- Molecule
- Karilysin long form Kly38; Tannerella forsythia potempin A (PotA)
- UniProt
- D0EM77, A0A1D3UV35
- Ligands
- ZN, CA
- Pockets
- 2 · best druggability 0.61
Structure
x-ray diffraction · resolution 1.35 · 2 distinct chains · 19% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Karilysin long form Kly38 | protein | 166 | 28% helix, 19% strand | D0EM77 |
| I | Tannerella forsythia potempin A (PotA) | protein | 94 | 3% helix, 56% strand | A0A1D3UV35 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, I
- CA · Calcium ion · metal · chains A
- GOL · Glycerol · additive · 2 copies · chains A, I
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A, I
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 | 256 | 0.61 | 0.80 | 44 | MES |
| 2 | 75 | 0.28 | 0.72 | 17 | empty |
Interfaces
1 interface between chains.
- A–I · 871 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- D0EM77 · AlphaFold monomer V2.0 prediction for karilysin (D0EM77) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 D0EM77
- Every structure of UniProt A0A1D3UV35
- Elsewhere: RCSB PDB 8B2Q · PDBe 8B2Q · UniProt D0EM77 · UniProt A0A1D3UV35
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.