MolNFT v1 · #154182 · protein
Structural basis of glycan recognition in globally predominant human P[8] rotavirus
6K2N · Outer capsid protein VP4: “Structural basis of glycan recognition in globally predominant human P[8] rotavirus”. X-ray diffraction, 3 ligands (A2G, GAL, NAG), 9 pockets (best druggability 0.89). MolNFT v1 #154182 on GenesisL1: 3D…
- PDB
- 6K2N
- Type
- protein
- Length
- 960 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Outer capsid protein VP4
- UniProt
- E2EA82
- Ligands
- A2G, GAL, NAG
- Pockets
- 9 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 8% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Outer capsid protein VP4 | protein | 160 | 8% helix, 57% strand | E2EA82 |
Ligands and binding sites
- A2G · 2-acetamido-2-deoxy-alpha-D-galactopyranose · sugar · 2 copies · chains B, D
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains B, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1032 | 0.89 | 0.91 | 188 | empty |
| 2 | 80 | 0.61 | 0.89 | 19 | empty |
| 3 | 70 | 0.58 | 0.89 | 22 | empty |
| 4 | 82 | 0.58 | 0.88 | 24 | empty |
| 5 | 67 | 0.57 | 0.88 | 24 | empty |
Interfaces
12 interfaces between chains.
- B–F · 496 Ų buried · 8 hydrogen bonds · protein-protein
- C–F · 473 Ų buried · 8 hydrogen bonds · protein-protein
- D–E · 471 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 464 Ų buried · 9 hydrogen bonds · protein-protein
- A–E · 458 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6K2N · Structural basis of glycan recognition in globally predominant human P[8] rotavirus · 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 E2EA82
- Elsewhere: RCSB PDB 6K2N · PDBe 6K2N · UniProt E2EA82
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