Research workbench
Crystal structure of the epstein-barr virus protein zebra (BZLF1, zta) bound to a methylated DNA duplex
Analyse Crystal structure of the epstein-barr virus protein zebra (BZLF1, zta) bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NX5
- Type
- protein + DNA
- Length
- 303 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trans-activator protein BZLF1; MEZRE2 DNA (bottom strand); MEZRE2 DNA (top strand)
- UniProt
- P03206
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 6 distinct chains · 76% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | Trans-activator protein BZLF1 | protein | 62 | 81% helix, 0% strand | P03206 |
| B, E | Trans-activator protein BZLF1 | protein | 61 | 72% helix, 0% strand | P03206 |
| C | MEZRE2 DNA (bottom strand) | dna | 16 | — | — |
| D | MEZRE2 DNA (top strand) | dna | 16 | — | — |
| G | MEZRE2 DNA (bottom strand) | dna | 13 | — | — |
| H | MEZRE2 DNA (top strand) | dna | 12 | — | — |
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 279 | 0.76 | 0.88 | 24 | empty |
| 2 | 258 | 0.74 | 0.88 | 27 | empty |
| 3 | 201 | 0.48 | 0.75 | 27 | empty |
| 4 | 117 | 0.42 | 0.76 | 14 | empty |
Interfaces
14 interfaces between chains.
- A–B · 1416 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 1255 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 714 Ų buried · 64 hydrogen bonds · nucleic-nucleic
- G–H · 509 Ų buried · 47 hydrogen bonds · nucleic-nucleic
- A–C · 409 Ų buried · 6 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 7NX5 · Crystal structure of the Epstein-Barr Virus protein ZEBRA (BZLF1, Zta) bound to a… · 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 7NX5 · PDBe 7NX5 · UniProt P03206
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