MolNFT v1 · #187479 · protein
XPA5 TCR in complex with HLA-DQ2-ALPHA1
7SG1 · HLA class II histocompatibility antigen, dq alpha 1 chain: “XPA5 TCR in complex with HLA-DQ2-ALPHA1”. X-ray diffraction, 2 ligands (NAG, CA), 20 pockets (best druggability 0.72). MolNFT v1 #187479 on GenesisL1: 3D structure, binding…
- PDB
- 7SG1
- Type
- protein
- Length
- 1,572 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; MHC class II HLA-dq-beta-1…
- UniProt
- P01909, O19712
- Ligands
- NAG, CA
- Pockets
- 20 · best druggability 0.72
Structure
x-ray diffraction · 9 distinct chains · 10% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class II histocompatibility antigen, dq alpha 1 chain | protein | 180 | 13% helix, 44% strand | P01909 |
| B | MHC class II HLA-dq-beta-1 | protein | 174 | 21% helix, 45% strand | O19712 |
| F | HLA class II histocompatibility antigen, dq alpha 1 chain | protein | 181 | 13% helix, 43% strand | P01909 |
| G | MHC class II HLA-dq-beta-1 | protein | 179 | 19% helix, 45% strand | O19712 |
| D | T-cell receptor, XPA5, alpha chain | protein | 193 | 3% helix, 40% strand | — |
| E | T-cell receptor, XPA5, beta chain | protein | 244 | 5% helix, 48% strand | — |
| C, H | DQ2-glia-ALPHA1A peptide | protein | 15 | 0% helix, 0% strand | — |
| I | T-cell receptor, XPA5, alpha chain | protein | 156 | 2% helix, 42% strand | — |
| J | T-cell receptor, XPA5, beta chain | protein | 235 | 4% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, F
- CA · Calcium ion · metal · 2 copies · chains A, F, E
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B, F, 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 | 1005 | 0.72 | 0.76 | 83 | empty |
| 2 | 1115 | 0.71 | 0.75 | 113 | empty |
| 3 | 166 | 0.51 | 0.78 | 30 | EDO |
| 4 | 151 | 0.48 | 0.78 | 27 | empty |
| 5 | 145 | 0.47 | 0.77 | 26 | EDO |
Interfaces
24 interfaces between chains.
- A–B · 2643 Ų buried · 49 hydrogen bonds · protein-protein
- F–G · 2635 Ų buried · 44 hydrogen bonds · protein-protein
- D–E · 1986 Ų buried · 17 hydrogen bonds · protein-protein
- I–J · 1658 Ų buried · 12 hydrogen bonds · protein-protein
- B–G · 749 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 15 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
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 P01909
- Every structure of UniProt O19712
- Elsewhere: RCSB PDB 7SG1 · PDBe 7SG1 · UniProt P01909 · UniProt O19712
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