MolNFT v1 · #187027 · protein
CD1A-endo-gdtcr complex
7RYM · T-cell surface glycoprotein CD1A: “CD1A-endo-gdtcr complex”. X-ray diffraction, 1 ligand (SO4), 13 pockets (best druggability 0.84). MolNFT v1 #187027 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7RYM
- Type
- protein
- Length
- 732 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
- SO4
- Pockets
- 13 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 10% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | T-cell surface glycoprotein CD1A | protein | 269 | 26% helix, 40% 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 | 235 | 2% helix, 40% strand | A0A0C4DH28, P01850 |
| D | T cell receptor delta variable 1,T cell receptor alpha chain constant | protein | 129 | 0% helix, 40% strand | A0A1B0GX56, P01848 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 614 | 0.84 | 0.89 | 47 | empty |
| 2 | 418 | 0.70 | 0.81 | 46 | empty |
| 3 | 320 | 0.63 | 0.79 | 37 | empty |
| 4 | 475 | 0.61 | 0.75 | 42 | empty |
| 5 | 148 | 0.58 | 0.82 | 30 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1353 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1291 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 400 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 267 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 228 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 7RYM · CD1a-endo-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 0.52
- 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 0.39
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 7RYM · PDBe 7RYM · UniProt P06126 · UniProt P61769 · UniProt A0A0C4DH28 · UniProt P01850 · UniProt A0A1B0GX56 · UniProt P01848
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