MolNFT v1 · #24965 · protein
Crystal structure of artocarpin-mannotriose complex
1VBO: “Crystal structure of artocarpin-mannotriose complex”. X-ray diffraction, 1 ligand (MAN), 5 pockets (best druggability 0.81). MolNFT v1 #24965 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1VBO
- Type
- protein
- Length
- 1,192 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Artocarpin
- UniProt
- Q7M1T4
- Ligands
- MAN
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 0% helix, 62% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Artocarpin | protein | 149 | 0% helix, 62% strand | Q7M1T4 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 20 copies · chains A, H, B, C, E, G, D, F
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 | 443 | 0.81 | 0.89 | 68 | empty |
| 2 | 502 | 0.79 | 0.86 | 77 | empty |
| 3 | 1005 | 0.75 | 0.78 | 83 | empty |
| 4 | 86 | 0.40 | 0.78 | 21 | MAN |
| 5 | 84 | 0.33 | 0.74 | 20 | empty |
Interfaces
16 interfaces between chains.
- C–D · 984 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 963 Ų buried · 21 hydrogen bonds · protein-protein
- E–F · 957 Ų buried · 20 hydrogen bonds · protein-protein
- G–H · 956 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 759 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (nonstandard).
Compared structures
- 1VBO · Crystal structure of artocarpin-mannotriose complex · 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 Q7M1T4
- Elsewhere: RCSB PDB 1VBO · PDBe 1VBO · UniProt Q7M1T4
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