MolNFT v1 · #187480 · protein
XPA5 TCR in complex with HLA-DQ2-OMEGA1
7SG2 · HLA class II histocompatibility antigen, dq alpha 1 chain: “XPA5 TCR in complex with HLA-DQ2-OMEGA1”. X-ray diffraction, 2 ligands (NAG, CA), 20 pockets (best druggability 0.72). MolNFT v1 #187480 on GenesisL1: 3D structure, binding…
- PDB
- 7SG2
- Type
- protein
- Length
- 1,569 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, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class II histocompatibility antigen, dq alpha 1 chain | protein | 178 | 15% helix, 43% strand | P01909 |
| B | MHC class II HLA-dq-beta-1 | protein | 175 | 21% helix, 46% strand | O19712 |
| F | HLA class II histocompatibility antigen, dq alpha 1 chain | protein | 178 | 15% helix, 46% strand | P01909 |
| G | MHC class II HLA-dq-beta-1 | protein | 180 | 20% helix, 45% strand | O19712 |
| D | T-cell receptor, XPA5, alpha chain | protein | 188 | 3% helix, 43% strand | — |
| E | T-cell receptor, XPA5, beta chain | protein | 242 | 6% helix, 48% strand | — |
| C, H | DQ2-glia-OMEGA1 peptide | protein | 13 | 0% helix, 0% strand | — |
| I | T-cell receptor, XPA5, alpha chain | protein | 170 | 4% helix, 45% strand | — |
| J | T-cell receptor, XPA5, beta chain | protein | 232 | 4% helix, 50% 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 B, E
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, J
- ACT · Acetate ion · additive · 2 copies · chains A, B, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 983 | 0.72 | 0.76 | 87 | empty |
| 2 | 944 | 0.70 | 0.75 | 84 | empty |
| 3 | 660 | 0.66 | 0.75 | 64 | empty |
| 4 | 369 | 0.56 | 0.74 | 48 | empty |
| 5 | 366 | 0.55 | 0.74 | 48 | empty |
Interfaces
24 interfaces between chains.
- F–G · 2543 Ų buried · 46 hydrogen bonds · protein-protein
- A–B · 2536 Ų buried · 48 hydrogen bonds · protein-protein
- D–E · 1977 Ų buried · 20 hydrogen bonds · protein-protein
- I–J · 1826 Ų buried · 24 hydrogen bonds · protein-protein
- B–G · 742 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 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 7SG2 · PDBe 7SG2 · UniProt P01909 · UniProt O19712
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