MolNFT v1 · #52811 · protein
Canine adenovirus 2 fibre head in complex with sialic acid
2WBV · Fiber protein: “Canine adenovirus 2 fibre head in complex with sialic acid”. X-ray diffraction, 2 ligands (SIA, GAL), 12 pockets (best druggability 0.84). MolNFT v1 #52811 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 2WBV
- Type
- protein
- Length
- 1,102 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fiber protein
- UniProt
- Q65914
- Ligands
- SIA, GAL
- Pockets
- 12 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 9% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Fiber protein | protein | 183 | 8% helix, 45% strand | Q65914 |
| B | Fiber protein | protein | 186 | 10% helix, 44% strand | Q65914 |
| D, F | Fiber protein | protein | 184 | 8% helix, 45% strand | Q65914 |
| E | Fiber protein | protein | 182 | 8% helix, 45% strand | Q65914 |
Ligands and binding sites
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 6 copies · chains D, A, B, C, E, F
- GAL · beta-D-galactopyranose · sugar · chains D
- GOL · Glycerol · additive · 6 copies · chains A, D, B, C, F, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 728 | 0.84 | 0.87 | 68 | empty |
| 2 | 763 | 0.83 | 0.86 | 64 | empty |
| 3 | 828 | 0.74 | 0.78 | 66 | GOL |
| 4 | 176 | 0.61 | 0.83 | 25 | empty |
| 5 | 197 | 0.59 | 0.81 | 29 | GOL |
Interfaces
7 interfaces between chains.
- C–F · 1228 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 1223 Ų buried · 22 hydrogen bonds · protein-protein
- C–E · 1205 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 1201 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1185 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 2WBV · Canine adenovirus 2 fibre head in complex with sialic acid · 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 Q65914
- Elsewhere: RCSB PDB 2WBV · PDBe 2WBV · UniProt Q65914
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