MolNFT v1 · #135983 · protein
The 2.8 a electron microscopy structure of adeno-associated virus-dj bound by a heparanoid pentasaccharide
5UF6 · Capsid protein VP1: “The 2.8 a electron microscopy structure of adeno-associated virus-dj bound by a heparanoid pentasaccharide”. Electron microscopy, 5 ligands (ZDO, SUS, IDS), 6 pockets (best druggability 0.64). MolNFT v1 #135983…
- PDB
- 5UF6
- Type
- protein
- Length
- 517 residues
- Chains
- 1
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein VP1
- Ligands
- ZDO, SUS, IDS, BDP, SGN
- Pockets
- 6 · best druggability 0.64
Structure
electron microscopy · 1 distinct chain · 5% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein VP1 | protein | 517 | 5% helix, 33% strand | — |
Ligands and binding sites
- ZDO · methyl 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranoside · ligand · chains A
- SUS · 2-deoxy-3,6-di-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose · ligand · chains A
- IDS · 2-O-sulfo-alpha-L-idopyranuronic acid · sugar · chains A
- BDP · beta-D-glucopyranuronic acid · sugar
- SGN · 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 547 | 0.64 | 0.76 | 58 | empty |
| 2 | 304 | 0.57 | 0.76 | 45 | empty |
| 3 | 110 | 0.43 | 0.77 | 24 | empty |
| 4 | 136 | 0.39 | 0.74 | 20 | empty |
| 5 | 116 | 0.37 | 0.74 | 19 | empty |
Compared structures
- 5UF6 · The 2.8 A Electron Microscopy Structure of Adeno-Associated Virus-DJ Bound by a… · 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
- Elsewhere: RCSB PDB 5UF6 · PDBe 5UF6
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