MolNFT v1 · #120317 · protein
Structure of myroilysin
5GWD: “Structure of myroilysin”. X-ray diffraction, 1 ligand (ZN), 7 pockets (best druggability 0.69). MolNFT v1 #120317 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5GWD
- Type
- protein
- Length
- 478 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Myroilysin
- UniProt
- A0A0P0DZ84
- Ligands
- ZN
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Myroilysin | protein | 239 | 33% helix, 11% strand | A0A0P0DZ84 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
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 | 89 | 0.69 | 0.93 | 24 | empty |
| 2 | 100 | 0.67 | 0.91 | 26 | empty |
| 3 | 86 | 0.53 | 0.85 | 22 | empty |
| 4 | 191 | 0.47 | 0.75 | 25 | empty |
| 5 | 179 | 0.46 | 0.75 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 45 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (methylation).
Compared structures
- 5GWD · Structure of Myroilysin · 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 A0A0P0DZ84
- Elsewhere: RCSB PDB 5GWD · PDBe 5GWD · UniProt A0A0P0DZ84
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