Research workbench
Crystal structure of human vascular adhesion protein-1 in complex with pyridazi inhibitors
Analyse Crystal structure of human vascular adhesion protein-1 in complex with pyridazi… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BTX
- Type
- protein
- Length
- 1,415 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.78
- Source
- HOMO SAPIENS
- Molecule
- Membrane primary amine oxidase
- EC
- 1.4.3.21
- UniProt
- Q16853
- Ligands
- WF8, NAG, MAN, BMA, CA, CU
- Pockets
- 18 · best druggability 0.86
Structure
x-ray diffraction · resolution 2.78 · 2 distinct chains · 15% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Membrane primary amine oxidase (EC 1.4.3.21) | protein | 709 | 16% helix, 40% strand | Q16853 |
| B | Membrane primary amine oxidase (EC 1.4.3.21) | protein | 706 | 15% helix, 40% strand | Q16853 |
Ligands and binding sites
- WF8 · 5-isopropylamino-2-phenyl-6-(1H-1,2,4-triazol-5-yl)-3(2H)-pyridazinone · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains B
- BMA · beta-D-mannopyranose · sugar
- CA · Calcium ion · metal · 4 copies · chains A, B
- CU · Copper (II) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 460 | 0.86 | 0.93 | 49 | empty |
| 2 | 480 | 0.79 | 0.86 | 52 | empty |
| 3 | 439 | 0.78 | 0.87 | 46 | empty |
| 4 | 780 | 0.78 | 0.82 | 60 | empty |
| 5 | 326 | 0.74 | 0.86 | 56 | empty |
Interfaces
1 interface between chains.
- A–B · 8515 Ų buried · 121 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 glycan, 7 disulfide, 2 modified (N-glycosylation, disulfide, nonstandard).
Compared structures
- 4BTX · Crystal structure of human vascular adhesion protein-1 in complex with pyridazinone… · the same entry in another collection · chain A against A, TM-score 1.00
- Q16853 · AlphaFold monomer V2.0 prediction for membrane primary amine oxidase (Q16853) · a predicted model of the same protein · 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 Q16853
- Elsewhere: RCSB PDB 4BTX · PDBe 4BTX · UniProt Q16853
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