Research workbench
Structure of the epstein-barr virus GP42 protein bound to the MHC class II receptor HLA-DR1
Analyse Structure of the epstein-barr virus GP42 protein bound to the MHC class II… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1KG0
- Type
- protein
- Length
- 517 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class II receptor HLA-DR1; Hemagglutinin ha peptide; GP42 protein
- UniProt
- P01903, P04229, P03205
- Pockets
- 4 · best druggability 0.41
Structure
x-ray diffraction · 4 distinct chains · 14% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MHC class II receptor HLA-DR1 | protein | 180 | 14% helix, 46% strand | P01903 |
| B | MHC class II receptor HLA-DR1 | protein | 188 | 18% helix, 46% strand | P04229 |
| D | Hemagglutinin ha peptide | protein | 13 | 0% helix, 8% strand | — |
| C | GP42 protein | protein | 136 | 11% helix, 24% strand | P03205 |
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 150 | 0.41 | 0.73 | 18 | empty |
| 2 | 85 | 0.33 | 0.74 | 17 | empty |
| 3 | 65 | 0.31 | 0.75 | 14 | empty |
| 4 | 74 | 0.30 | 0.73 | 21 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2565 Ų buried · 38 hydrogen bonds · protein-protein
- A–D · 688 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 682 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 547 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 1KG0 · Structure of the Epstein-Barr Virus gp42 Protein Bound to the MHC class II Receptor… · the same entry in another collection · chain A against A, TM-score 1.00
- P01903 · AlphaFold monomer V2.0 prediction for HLA class II histocompatibility antigen, dr alpha… · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P01903
- Every structure of UniProt P04229
- Every structure of UniProt P03205
- Elsewhere: RCSB PDB 1KG0 · PDBe 1KG0 · UniProt P01903 · UniProt P04229 · UniProt P03205
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