Research workbench
Cryo-EM structure of EBV BFLF1
Analyse Cryo-EM structure of EBV BFLF1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XFA
- Type
- protein
- Length
- 4,060 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Packaging protein UL32
- UniProt
- A0A2D1LYN0
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 1 distinct chain · 52% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J | Packaging protein UL32 | protein | 406 | 52% helix, 2% strand | A0A2D1LYN0 |
Ligands and binding sites
- ZN · Zinc ion · metal · 20 copies · chains A, B, C, D, E, F, G, H, I, J
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 | 259 | 0.80 | 0.92 | 43 | empty |
| 2 | 260 | 0.79 | 0.91 | 44 | empty |
| 3 | 260 | 0.79 | 0.91 | 45 | empty |
| 4 | 387 | 0.78 | 0.87 | 57 | empty |
| 5 | 380 | 0.77 | 0.87 | 56 | empty |
Interfaces
15 interfaces between chains.
- F–J · 1334 Ų buried · 10 hydrogen bonds · protein-protein
- D–E · 1333 Ų buried · 10 hydrogen bonds · protein-protein
- G–H · 1332 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1324 Ų buried · 10 hydrogen bonds · protein-protein
- H–I · 1323 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6XFA · Cryo-EM structure of EBV BFLF1 · the same entry in another collection · chain I against I, 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 A0A2D1LYN0
- Elsewhere: RCSB PDB 6XFA · PDBe 6XFA · UniProt A0A2D1LYN0
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