MolNFT v1 · #179736 · protein
DQA1*01:02/DQB1*06:02 in complex with a hemagglutinin peptide from the H1N1 pandemic flu virus.
7KEI · MHC class II HLA-dq-alpha chain: “DQA1*01:02/DQB1*06:02 in complex with a hemagglutinin peptide from the H1N1 pandemic flu virus.”. X-ray diffraction, 3 ligands (NAG, BMA, FUC), 2 pockets (best druggability 0.52). MolNFT v1 #179736…
- PDB
- 7KEI
- Type
- protein
- Length
- 382 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class II HLA-dq-alpha chain; HLA class II histocompatibility antigen, dq beta 1…
- UniProt
- Q30066, Q5SU54
- Ligands
- NAG, BMA, FUC
- Pockets
- 2 · best druggability 0.52
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MHC class II HLA-dq-alpha chain | protein | 182 | 15% helix, 45% strand | Q30066 |
| B | HLA class II histocompatibility antigen, dq beta 1 chain | protein | 180 | 22% helix, 45% strand | Q5SU54 |
| C | Ha peptide from 2009 H1N1 pandemic flu virus. | protein | 20 | 0% helix, 10% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B, C
- BMA · beta-D-mannopyranose · sugar
- FUC · alpha-L-fucopyranose · sugar · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 259 | 0.52 | 0.75 | 41 | empty |
| 2 | 80 | 0.33 | 0.74 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2722 Ų buried · 51 hydrogen bonds · protein-protein
- A–C · 774 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 619 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 7KEI · DQA1*01:02/DQB1*06:02 in complex with a hemagglutinin peptide from the H1N1 pandemic flu… · 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 Q30066
- Every structure of UniProt Q5SU54
- Elsewhere: RCSB PDB 7KEI · PDBe 7KEI · UniProt Q30066 · UniProt Q5SU54
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