Research workbench
SV40 VP1 pentamer in complex with GM1 oligosaccharide
Analyse SV40 VP1 pentamer in complex with GM1 oligosaccharide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BWR
- Type
- protein
- Length
- 1,318 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein VP1
- UniProt
- P03087
- Ligands
- GAL, BGC, NGA, SIA
- Pockets
- 14 · best druggability 0.65
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Capsid protein VP1 | protein | 267 | 7% helix, 39% strand | P03087 |
| B | Capsid protein VP1 | protein | 255 | 7% helix, 42% strand | P03087 |
| D | Capsid protein VP1 | protein | 265 | 7% helix, 41% strand | P03087 |
| E | Capsid protein VP1 | protein | 264 | 8% helix, 42% strand | P03087 |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · 6 copies · chains A, E, B, C, D
- BGC · beta-D-glucopyranose · sugar · 3 copies
- NGA · 2-acetamido-2-deoxy-beta-D-galactopyranose · sugar · 3 copies · chains A, C, D, E
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 3 copies · chains A, B, C, D, E
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, E, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 90 | 0.65 | 0.91 | 23 | EDO |
| 2 | 79 | 0.62 | 0.90 | 24 | EDO |
| 3 | 415 | 0.60 | 0.76 | 56 | empty |
| 4 | 56 | 0.60 | 0.91 | 22 | empty |
| 5 | 80 | 0.59 | 0.88 | 22 | EDO |
Interfaces
5 interfaces between chains.
- D–E · 2331 Ų buried · 39 hydrogen bonds · protein-protein
- A–B · 2320 Ų buried · 39 hydrogen bonds · protein-protein
- C–D · 2318 Ų buried · 39 hydrogen bonds · protein-protein
- A–E · 2309 Ų buried · 43 hydrogen bonds · protein-protein
- B–C · 2299 Ų buried · 35 hydrogen bonds · protein-protein
Compared structures
- 3BWR · SV40 VP1 pentamer in complex with GM1 oligosaccharide · 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 P03087
- Elsewhere: RCSB PDB 3BWR · PDBe 3BWR · UniProt P03087
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