Research workbench
CD1A-sulfatide-gdtcr complex
Analyse CD1A-sulfatide-gdtcr complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RYN
- Type
- protein
- Length
- 781 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- T-cell surface glycoprotein CD1A; Beta-2-microglobulin; T cell receptor gamma variable…
- UniProt
- P06126, P61769, A0A0C4DH28, P01850, A0A1B0GX56, P01848
- Ligands
- CIS, NAG, SO4
- Pockets
- 6 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 12% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | T-cell surface glycoprotein CD1A | protein | 271 | 28% helix, 39% strand | P06126 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| C | T cell receptor gamma variable 4,T cell receptor beta constant 1 | protein | 238 | 7% helix, 48% strand | A0A0C4DH28, P01850 |
| D | T cell receptor delta variable 1,T cell receptor alpha chain constant | protein | 173 | 2% helix, 45% strand | A0A1B0GX56, P01848 |
Ligands and binding sites
- CIS · (15Z)-N-((1S,2R,3E)-2-hydroxy-1-{[(3-O-sulfo-beta-D-galactopyranosyl)oxy]methyl}heptadec-3-enyl)tetracos-15-enamide · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A, C
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 629 | 0.85 | 0.89 | 51 | CIS |
| 2 | 1188 | 0.71 | 0.75 | 116 | empty |
| 3 | 539 | 0.71 | 0.80 | 62 | SO4 |
| 4 | 463 | 0.66 | 0.78 | 44 | EDO |
| 5 | 155 | 0.47 | 0.77 | 32 | EDO |
Interfaces
5 interfaces between chains.
- C–D · 1884 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1361 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 264 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 264 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 249 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7RYN · CD1a-sulfatide-gdTCR complex · the same entry in another collection · chain D against D, TM-score 1.00
- P06126 · AlphaFold monomer V2.0 prediction for T-cell surface glycoprotein CD1A (P06126) · a predicted model of the same protein · chain A against A, TM-score 0.97
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain B against A, TM-score 0.95
- P01850 · AlphaFold monomer V2.0 prediction for T cell receptor beta constant 1 (P01850) · a predicted model of the same protein · chain C against A, TM-score 0.53
- P01848 · AlphaFold monomer V2.0 prediction for T cell receptor alpha chain constant (P01848) · a predicted model of the same protein · chain D against A, TM-score 0.30
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 P06126
- Every structure of UniProt P61769
- Every structure of UniProt A0A0C4DH28
- Every structure of UniProt P01850
- Every structure of UniProt A0A1B0GX56
- Every structure of UniProt P01848
- Elsewhere: RCSB PDB 7RYN · PDBe 7RYN · UniProt P06126 · UniProt P61769 · UniProt A0A0C4DH28 · UniProt P01850 · UniProt A0A1B0GX56 · UniProt P01848
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