Research workbench
Structural basis for cooperative binding of EBNA1 to the epstein-barr virus dyad symmetry minimal origin of replication
Analyse Structural basis for cooperative binding of EBNA1 to the epstein-barr virus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PW2
- Type
- protein + DNA
- Length
- 1,384 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Epstein-barr nuclear antigen 1; DNA (62-mer); DNA (62-mer) complementary DNA strand
- UniProt
- P03211
- Pockets
- 18 · best druggability 0.74
Structure
x-ray diffraction · 5 distinct chains · 32% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, I, J, K, L | Epstein-barr nuclear antigen 1 | protein | 147 | 32% helix, 26% strand | P03211 |
| E | DNA (62-mer) | dna | 57 | — | — |
| F | DNA (62-mer) complementary DNA strand | dna | 53 | — | — |
| G | DNA (62-mer) | dna | 49 | — | — |
| H | DNA (62-mer) complementary DNA strand | dna | 49 | — | — |
Pockets
18 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 82 | 0.74 | 0.98 | 19 | empty |
| 2 | 66 | 0.72 | 0.98 | 18 | empty |
| 3 | 54 | 0.71 | 0.99 | 15 | empty |
| 4 | 299 | 0.70 | 0.85 | 32 | empty |
| 5 | 335 | 0.69 | 0.83 | 37 | empty |
Interfaces
25 interfaces between chains.
- K–L · 2331 Ų buried · 24 hydrogen bonds · protein-protein
- E–F · 2329 Ų buried · 179 hydrogen bonds · nucleic-nucleic
- I–J · 2328 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 2310 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 2268 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 6PW2 · Structural Basis for Cooperative Binding of EBNA1 to the Epstein-Barr Virus Dyad Symmetry… · 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 P03211
- Elsewhere: RCSB PDB 6PW2 · PDBe 6PW2 · UniProt P03211
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