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Crystal structure of the hexameric ring of epstein-barr virus nuclear antigen-1, EBNA1
Analyse Crystal structure of the hexameric ring of epstein-barr virus nuclear… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WMF
- Type
- protein
- Length
- 824 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Epstein-barr nuclear antigen 1
- UniProt
- P03211
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Epstein-barr nuclear antigen 1 | protein | 137 | 32% helix, 28% strand | P03211 |
| C | Epstein-barr nuclear antigen 1 | protein | 138 | 33% helix, 28% strand | P03211 |
| E | Epstein-barr nuclear antigen 1 | protein | 135 | 33% helix, 28% strand | P03211 |
| F | Epstein-barr nuclear antigen 1 | protein | 140 | 34% helix, 27% strand | P03211 |
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 563 | 0.77 | 0.84 | 69 | empty |
| 2 | 363 | 0.69 | 0.82 | 52 | empty |
| 3 | 103 | 0.43 | 0.77 | 22 | empty |
| 4 | 116 | 0.43 | 0.76 | 21 | empty |
| 5 | 122 | 0.40 | 0.75 | 21 | empty |
Interfaces
15 interfaces between chains.
- C–D · 2430 Ų buried · 23 hydrogen bonds · protein-protein
- E–F · 2426 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 2386 Ų buried · 25 hydrogen bonds · protein-protein
- B–D · 301 Ų buried · 2 hydrogen bonds · protein-protein
- A–F · 296 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5WMF · Crystal structure of the Hexameric Ring of Epstein-Barr Virus Nuclear Antigen-1, EBNA1 · the same entry in another collection · chain C against C, 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 5WMF · PDBe 5WMF · UniProt P03211
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