Research workbench
A viral peptide from MAREK'S disease virus bound to chicken MHC-II molecule
Analyse A viral peptide from MAREK'S disease virus bound to chicken MHC-II molecule in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7PDY
- Type
- protein
- Length
- 1,165 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class II alpha chain; 38 kda PHOSPHOPROTEIN,MHC class II beta chain
- UniProt
- Q4U5Z6, P68348, Q4U5Z9
- Ligands
- NAG
- Pockets
- 10 · best druggability 0.77
Structure
x-ray diffraction · 6 distinct chains · 16% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MHC class II alpha chain | protein | 187 | 14% helix, 48% strand | Q4U5Z6 |
| B | 38 kda PHOSPHOPROTEIN,MHC class II beta chain | protein | 204 | 18% helix, 44% strand | P68348, Q4U5Z9 |
| C | MHC class II alpha chain | protein | 184 | 13% helix, 48% strand | Q4U5Z6 |
| D | 38 kda PHOSPHOPROTEIN,MHC class II beta chain | protein | 202 | 17% helix, 44% strand | P68348, Q4U5Z9 |
| E | MHC class II alpha chain | protein | 184 | 15% helix, 49% strand | Q4U5Z6 |
| F | 38 kda PHOSPHOPROTEIN,MHC class II beta chain | protein | 204 | 17% helix, 42% strand | P68348, Q4U5Z9 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains E, F, A, C, D
- ACT · Acetate ion · additive · 7 copies · chains A, B, C, E, D, F
- GOL · Glycerol · additive · 5 copies · chains A, B, C, E, F
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 907 | 0.77 | 0.80 | 95 | ACT |
| 2 | 766 | 0.75 | 0.80 | 73 | empty |
| 3 | 168 | 0.62 | 0.84 | 29 | empty |
| 4 | 179 | 0.57 | 0.81 | 30 | empty |
| 5 | 247 | 0.52 | 0.75 | 26 | GOL |
Interfaces
8 interfaces between chains.
- A–B · 3159 Ų buried · 50 hydrogen bonds · protein-protein
- E–F · 3114 Ų buried · 51 hydrogen bonds · protein-protein
- C–D · 2869 Ų buried · 49 hydrogen bonds · protein-protein
- C–F · 736 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 674 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 7PDY · A viral peptide from Marek's disease virus bound to chicken MHC-II molecule · 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 Q4U5Z6
- Every structure of UniProt P68348
- Every structure of UniProt Q4U5Z9
- Elsewhere: RCSB PDB 7PDY · PDBe 7PDY · UniProt Q4U5Z6 · UniProt P68348 · UniProt Q4U5Z9
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