MolNFT v1 · #24335 · protein
Crystal structure of human vascular adhesion protein-1
1US1 · Membrane copper amine oxidase: “Crystal structure of human vascular adhesion protein-1”. X-ray diffraction, 3 ligands (NAG, CA, CU), 17 pockets (best druggability 0.87). MolNFT v1 #24335 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1US1
- Type
- protein
- Length
- 1,403 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Membrane copper amine oxidase
- EC
- 1.4.3.6
- UniProt
- Q16853
- Ligands
- NAG, CA, CU
- Pockets
- 17 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Membrane copper amine oxidase (EC 1.4.3.6) | protein | 704 | 16% helix, 40% strand | Q16853 |
| B | Membrane copper amine oxidase (EC 1.4.3.6) | protein | 699 | 15% helix, 41% strand | Q16853 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
- 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
17 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 473 | 0.87 | 0.94 | 49 | empty |
| 2 | 912 | 0.81 | 0.83 | 87 | empty |
| 3 | 478 | 0.80 | 0.87 | 46 | empty |
| 4 | 505 | 0.80 | 0.87 | 53 | empty |
| 5 | 484 | 0.74 | 0.82 | 53 | empty |
Interfaces
1 interface between chains.
- A–B · 8502 Ų buried · 114 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 4 glycan, 2 modified (disulfide, N-glycosylation, nonstandard).
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 Q16853
- Elsewhere: RCSB PDB 1US1 · PDBe 1US1 · UniProt Q16853
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