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
- 3GZU
- Type
- protein
- Length
- 6,742 residues
- Chains
- 15
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inner capsid protein VP2; Intermediate capsid protein VP6
- UniProt
- B2BMF8, P04509
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 3 distinct chains · 40% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Inner capsid protein VP2 | protein | 781 | 41% helix, 10% strand | B2BMF8 |
| B | Inner capsid protein VP2 | protein | 800 | 43% helix, 10% strand | B2BMF8 |
| C, D, E, F, G, H, I, J, K, L, M, N, O | Intermediate capsid protein VP6 | protein | 397 | 31% helix, 33% strand | P04509 |
Ligands and binding sites
- ZN · Zinc ion · metal · 5 copies · chains C, D, E, G, I, J, K, L, M, N, O
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 | 549 | 0.87 | 0.93 | 87 | empty |
| 2 | 538 | 0.87 | 0.93 | 90 | empty |
| 3 | 539 | 0.86 | 0.93 | 92 | empty |
| 4 | 525 | 0.86 | 0.93 | 77 | empty |
| 5 | 1056 | 0.86 | 0.87 | 118 | empty |
Interfaces
39 interfaces between chains.
- F–G · 2543 Ų buried · 36 hydrogen bonds · protein-protein
- L–M · 2542 Ų buried · 36 hydrogen bonds · protein-protein
- I–J · 2539 Ų buried · 36 hydrogen bonds · protein-protein
- M–N · 2538 Ų buried · 37 hydrogen bonds · protein-protein
- G–H · 2536 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
- 3GZU · VP7 recoated rotavirus DLP · 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 B2BMF8
- Every structure of UniProt P04509
- Elsewhere: RCSB PDB 3GZU · PDBe 3GZU · UniProt B2BMF8 · UniProt P04509
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