Research workbench
CD1A-dideoxymycobactin-gdtcr complex
Analyse CD1A-dideoxymycobactin-gdtcr complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RYO
- Type
- protein
- Length
- 806 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
- WGR, SO4
- Pockets
- 11 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 12% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | T-cell surface glycoprotein CD1A | protein | 277 | 30% helix, 39% strand | P06126 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 47% strand | P61769 |
| C | T cell receptor gamma variable 4,T cell receptor beta constant 1 | protein | 238 | 6% helix, 49% strand | A0A0C4DH28, P01850 |
| D | T cell receptor delta variable 1,T cell receptor alpha chain constant | protein | 192 | 2% helix, 45% strand | A0A1B0GX56, P01848 |
Ligands and binding sites
- WGR · dideoxymycobactin-838 · ligand · chains A
- SO4 · Sulfate ion · ion · chains C, D
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 667 | 0.84 | 0.88 | 49 | WGR |
| 2 | 1068 | 0.74 | 0.77 | 99 | SO4 |
| 3 | 481 | 0.67 | 0.78 | 52 | empty |
| 4 | 341 | 0.67 | 0.81 | 50 | empty |
| 5 | 134 | 0.52 | 0.81 | 26 | empty |
Interfaces
5 interfaces between chains.
- C–D · 2101 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1387 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 387 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 257 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 255 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 7RYO · CD1a-dideoxymycobactin-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 0.96
- 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 0.37
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 7RYO · PDBe 7RYO · UniProt P06126 · UniProt P61769 · UniProt A0A0C4DH28 · UniProt P01850 · UniProt A0A1B0GX56 · UniProt P01848
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