MolNFT v1 · #57869 · protein
Crystal structure of vascular adhesion protein-1 in space group C2
3ALA · Membrane primary amine oxidase: “Crystal structure of vascular adhesion protein-1 in space group C2”. X-ray diffraction, 6 ligands (NAG, BMA, FUL), 20 pockets (best druggability 0.87). MolNFT v1 #57869 on GenesisL1: 3D structure…
- PDB
- 3ALA
- Type
- protein
- Length
- 4,939 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Membrane primary amine oxidase
- EC
- 1.4.3.21
- UniProt
- Q16853
- Ligands
- NAG, BMA, FUL, FUC, CA, CU
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 7 distinct chains · 16% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Membrane primary amine oxidase (EC 1.4.3.21) | protein | 705 | 16% helix, 41% strand | Q16853 |
| B | Membrane primary amine oxidase (EC 1.4.3.21) | protein | 705 | 16% helix, 41% strand | Q16853 |
| C | Membrane primary amine oxidase (EC 1.4.3.21) | protein | 709 | 16% helix, 41% strand | Q16853 |
| D | Membrane primary amine oxidase (EC 1.4.3.21) | protein | 711 | 17% helix, 42% strand | Q16853 |
| E | Membrane primary amine oxidase (EC 1.4.3.21) | protein | 702 | 17% helix, 41% strand | Q16853 |
| F | Membrane primary amine oxidase (EC 1.4.3.21) | protein | 701 | 16% helix, 42% strand | Q16853 |
| G | Membrane primary amine oxidase (EC 1.4.3.21) | protein | 706 | 16% helix, 41% strand | Q16853 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 36 copies · chains A, B, C, D, E, F, G
- BMA · beta-D-mannopyranose · sugar · 7 copies
- FUL · beta-L-fucopyranose · sugar · 6 copies · chains A, B, C, E, F
- FUC · alpha-L-fucopyranose · sugar · chains G
- CA · Calcium ion · metal · 14 copies · chains A, B, C, D, E, F, G
- CU · Copper (II) ion · metal · 7 copies · chains A, B, C, D, E, F, G
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1091 | 0.87 | 0.88 | 115 | empty |
| 2 | 1154 | 0.86 | 0.87 | 117 | empty |
| 3 | 1107 | 0.86 | 0.87 | 93 | empty |
| 4 | 410 | 0.80 | 0.89 | 61 | empty |
| 5 | 436 | 0.79 | 0.87 | 47 | empty |
Interfaces
8 interfaces between chains.
- C–D · 8537 Ų buried · 123 hydrogen bonds · protein-protein
- A–B · 8396 Ų buried · 120 hydrogen bonds · protein-protein
- F–G · 8348 Ų buried · 119 hydrogen bonds · protein-protein
- B–E · 383 Ų buried · 3 hydrogen bonds · protein-protein
- B–F · 303 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 28 disulfide, 22 glycan, 7 modified (disulfide, N-glycosylation, nonstandard).
Compared structures
- 3ALA · Crystal structure of vascular adhesion protein-1 in space group C2 · the same entry in another collection · chain C against C, TM-score 1.00
- Q16853 · AlphaFold monomer V2.0 prediction for membrane primary amine oxidase (Q16853) · a predicted model of the same protein · chain E 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 3ALA · PDBe 3ALA · UniProt Q16853
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.