Research workbench
Structure of the epstein-barr virus zebra protein
Analyse Structure of the epstein-barr virus zebra protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2C9L
- Type
- protein + DNA
- Length
- 162 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*AP*AP*GP*CP*AP*CP*TP*GP*AP*CP *TP*CP*AP*TP*GP*AP*AP*GP*T)-3'…
- UniProt
- P03206
- Pockets
- 3 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5'-D(*AP*AP*GP*CP*AP*CP*TP*GP*AP*CP *TP*CP*AP*TP*GP*AP*AP*GP*T)-3' | dna | 19 | — | — |
| B | 5'-D(*AP*CP*TP*TP*CP*AP*CP*TP*GP*AP *GP*TP*CP*AP*GP*TP*GP*CP*T)-3' | dna | 18 | — | — |
| Y | BZLF1 trans-activator protein | protein | 63 | 81% helix, 0% strand | P03206 |
| Z | BZLF1 trans-activator protein | protein | 62 | 74% helix, 0% strand | P03206 |
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 228 | 0.75 | 0.90 | 26 | empty |
| 2 | 131 | 0.49 | 0.79 | 17 | empty |
| 3 | 120 | 0.42 | 0.76 | 17 | empty |
Interfaces
6 interfaces between chains.
- Y–Z · 1472 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 803 Ų buried · 83 hydrogen bonds · nucleic-nucleic
- B–Z · 371 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–Y · 356 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–Z · 303 Ų buried · 6 hydrogen bonds · protein-nucleic
Compared structures
- 2C9L · Structure of the Epstein-Barr virus ZEBRA protein · 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 P03206
- Elsewhere: RCSB PDB 2C9L · PDBe 2C9L · UniProt P03206
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