Research workbench
Structure of myroilysin
Analyse Structure of myroilysin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZJK
- Type
- protein
- Length
- 3,683 residues
- Chains
- 18
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Myroilysin
- UniProt
- A0A0P0DZ84
- Ligands
- ZN, PO4
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F, G, H, I, L, N, O, P, Q, R | Myroilysin | protein | 204 | 36% helix, 15% strand | A0A0P0DZ84 |
| B, K | Myroilysin | protein | 206 | 35% helix, 14% strand | A0A0P0DZ84 |
| C, D, E, M | Myroilysin | protein | 205 | 35% helix, 15% strand | A0A0P0DZ84 |
| J | Myroilysin | protein | 207 | 34% helix, 14% strand | A0A0P0DZ84 |
Ligands and binding sites
- ZN · Zinc ion · metal · 18 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R
- PO4 · Phosphate ion · ion · 12 copies · chains B, I, D, E, P, A, F, G, Q, H, N, J, K, M
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 940 | 0.78 | 0.80 | 94 | empty |
| 2 | 640 | 0.76 | 0.82 | 44 | empty |
| 3 | 916 | 0.75 | 0.78 | 76 | empty |
| 4 | 735 | 0.75 | 0.80 | 48 | empty |
| 5 | 806 | 0.73 | 0.78 | 72 | empty |
Interfaces
30 interfaces between chains.
- H–K · 790 Ų buried · 6 hydrogen bonds · protein-protein
- C–L · 790 Ų buried · 13 hydrogen bonds · protein-protein
- M–O · 771 Ų buried · 9 hydrogen bonds · protein-protein
- G–I · 764 Ų buried · 6 hydrogen bonds · protein-protein
- B–Q · 752 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5ZJK · 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 5ZJK · PDBe 5ZJK · UniProt A0A0P0DZ84
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