MolNFT v1 · #33326 · protein
Structure of the epstein-barr virus oncogene BARF1
2CH8 · 33 kda early protein: “Structure of the epstein-barr virus oncogene BARF1”. X-ray diffraction, 3 ligands (NAG, MAN, PT), 1 pocket (best druggability 0.47). MolNFT v1 #33326 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 2CH8
- Type
- protein
- Length
- 746 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 33 kda early protein
- UniProt
- P03228
- Ligands
- NAG, MAN, PT
- Pockets
- 1 · best druggability 0.47
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 62% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 33 kda early protein | protein | 188 | 5% helix, 62% strand | P03228 |
| B, C | 33 kda early protein | protein | 186 | 5% helix, 62% strand | P03228 |
| D | 33 kda early protein | protein | 186 | 5% helix, 62% strand | P03228 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B, C, D
- MAN · alpha-D-mannopyranose · sugar · 4 copies
- PT · Platinum (II) ion · metal · 12 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 87 | 0.47 | 0.81 | 21 | empty |
Interfaces
2 interfaces between chains.
- B–C · 1476 Ų buried · 26 hydrogen bonds · protein-protein
- A–D · 1430 Ų buried · 28 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 2CH8 · Structure of the Epstein-Barr Virus Oncogene BARF1 · 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 P03228
- Elsewhere: RCSB PDB 2CH8 · PDBe 2CH8 · UniProt P03228
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