Research workbench
Crystal structure of native protease nexin-1 with heparin
Analyse Crystal structure of native protease nexin-1 with heparin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DY0
- Type
- protein
- Length
- 732 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glia-derived nexin
- UniProt
- P07093
- Ligands
- IDS, SGN, SO4
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glia-derived nexin | protein | 362 | 31% helix, 32% strand | P07093 |
| B | Glia-derived nexin | protein | 370 | 31% helix, 33% strand | P07093 |
Ligands and binding sites
- IDS · 2-O-sulfo-alpha-L-idopyranuronic acid · sugar · chains A
- SGN · 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose · sugar · chains A
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 607 | 0.69 | 0.78 | 64 | empty |
| 2 | 54 | 0.58 | 0.91 | 17 | empty |
| 3 | 289 | 0.57 | 0.77 | 41 | empty |
| 4 | 136 | 0.45 | 0.77 | 26 | empty |
| 5 | 52 | 0.32 | 0.78 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 966 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
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 P07093
- Elsewhere: RCSB PDB 4DY0 · PDBe 4DY0 · UniProt P07093
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