Research workbench
VP7 recoated rotavirus dlp
Analyse VP7 recoated rotavirus dlp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GZT
- Type
- protein
- Length
- 3,315 residues
- Chains
- 13
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Outer capsid glycoprotein VP7
- UniProt
- P12476
- Ligands
- NAG, CA
- Pockets
- 20 · best druggability 0.78
Structure
electron microscopy · 1 distinct chain · 24% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, F, G, H, I, J, K, L, M, N, O, P, Q | Outer capsid glycoprotein VP7 | protein | 255 | 24% helix, 30% strand | P12476 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 26 copies · chains B, F, G, H, I, J, K, L, M, N, O, P, Q
- CA · Calcium ion · metal · 30 copies · chains B, F, G, H, I, J, K, L, M, N, O, P, Q
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 784 | 0.78 | 0.82 | 107 | empty |
| 2 | 559 | 0.76 | 0.83 | 101 | empty |
| 3 | 464 | 0.75 | 0.83 | 83 | empty |
| 4 | 529 | 0.74 | 0.82 | 86 | empty |
| 5 | 184 | 0.71 | 0.89 | 34 | empty |
Interfaces
15 interfaces between chains.
- M–N · 1409 Ų buried · 16 hydrogen bonds · protein-protein
- O–P · 1408 Ų buried · 16 hydrogen bonds · protein-protein
- I–K · 1407 Ų buried · 16 hydrogen bonds · protein-protein
- I–J · 1407 Ų buried · 16 hydrogen bonds · protein-protein
- L–N · 1407 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 52 disulfide, 12 isopeptide (disulfide, isopeptide).
Compared structures
- 3GZT · VP7 recoated rotavirus DLP · the same entry in another collection · chain B against B, 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 P12476
- Elsewhere: RCSB PDB 3GZT · PDBe 3GZT · UniProt P12476
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