MolNFT v1 · #53999 · protein
Equine rhinitis a virus in complex with its sialic acid receptor
2XBO · P1: “Equine rhinitis a virus in complex with its sialic acid receptor”. X-ray diffraction, 3 ligands (GLC, GAL, SIA), 9 pockets (best druggability 0.74). MolNFT v1 #53999 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2XBO
- Type
- protein
- Length
- 693 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- P1
- UniProt
- B9VV85
- Ligands
- GLC, GAL, SIA
- Pockets
- 9 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 8% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1 | P1 | protein | 246 | 4% helix, 27% strand | B9VV85 |
| 2 | P1 | protein | 200 | 10% helix, 39% strand | B9VV85 |
| 3 | P1 | protein | 226 | 8% helix, 35% strand | B9VV85 |
| 4 | P1 | protein | 21 | 33% helix, 10% strand | B9VV85 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar
- GAL · beta-D-galactopyranose · sugar
- SIA · N-acetyl-alpha-neuraminic acid · sugar · chains 1
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 68 | 0.74 | 0.98 | 18 | empty |
| 2 | 245 | 0.55 | 0.77 | 42 | empty |
| 3 | 78 | 0.50 | 0.83 | 14 | empty |
| 4 | 167 | 0.44 | 0.75 | 25 | empty |
| 5 | 120 | 0.39 | 0.75 | 27 | empty |
Interfaces
5 interfaces between chains.
- 1–3 · 3887 Ų buried · 45 hydrogen bonds · protein-protein
- 2–3 · 1316 Ų buried · 19 hydrogen bonds · protein-protein
- 1–2 · 1206 Ų buried · 19 hydrogen bonds · protein-protein
- 3–4 · 640 Ų buried · 5 hydrogen bonds · protein-protein
- 1–4 · 382 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 2XBO · Equine Rhinitis A Virus in Complex with its Sialic Acid Receptor · the same entry in another collection · chain 1 against 1, 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 B9VV85
- Elsewhere: RCSB PDB 2XBO · PDBe 2XBO · UniProt B9VV85
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