Research workbench
BEL502-DQ8-glia-ALPHA1 complex
Analyse BEL502-DQ8-glia-ALPHA1 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KS9
- Type
- protein
- Length
- 1,615 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class II histocompatibility antigen, dq alpha 1 chain; HLA class II…
- UniProt
- Q30063, U3PYM0
- Ligands
- NAG, CA
- Pockets
- 20 · best druggability 0.69
Structure
x-ray diffraction · 7 distinct chains · 10% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | HLA class II histocompatibility antigen, dq alpha 1 chain | protein | 182 | 15% helix, 45% strand | Q30063 |
| B | HLA class II histocompatibility antigen, dq beta 1 chain | protein | 181 | 17% helix, 44% strand | U3PYM0 |
| D | HLA class II histocompatibility antigen, dq beta 1 chain | protein | 173 | 20% helix, 45% strand | U3PYM0 |
| E | BEL502 TCR alpha TRAV20*01 | protein | 193 | 2% helix, 51% strand | — |
| F, H | BEL502 TCR beta TRBV9*01 | protein | 240 | 7% helix, 52% strand | — |
| G | BEL502 TCR alpha TRAV20*01 | protein | 192 | 2% helix, 48% strand | — |
| I, J | DQ8-glia-ALPHA1 peptide | protein | 16 | 0% helix, 13% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 4 copies · chains A, C, E, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 938 | 0.69 | 0.75 | 80 | empty |
| 2 | 899 | 0.69 | 0.75 | 84 | empty |
| 3 | 92 | 0.51 | 0.83 | 19 | empty |
| 4 | 205 | 0.48 | 0.75 | 28 | empty |
| 5 | 101 | 0.48 | 0.81 | 20 | empty |
Interfaces
21 interfaces between chains.
- C–D · 2641 Ų buried · 54 hydrogen bonds · protein-protein
- A–B · 2641 Ų buried · 53 hydrogen bonds · protein-protein
- E–F · 2113 Ų buried · 28 hydrogen bonds · protein-protein
- G–H · 1990 Ų buried · 23 hydrogen bonds · protein-protein
- D–I · 730 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 5KS9 · Bel502-DQ8-glia-alpha1 complex · 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 Q30063
- Every structure of UniProt U3PYM0
- Elsewhere: RCSB PDB 5KS9 · PDBe 5KS9 · UniProt Q30063 · UniProt U3PYM0
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