MolNFT v1 · #100100 · protein
Structure of the DP10.7 TCR with CD1D-sulfatide
4MNG · Beta-2-microglobulin: “Structure of the DP10.7 TCR with CD1D-sulfatide”. X-ray diffraction, 2 ligands (CIS, NAG), 9 pockets (best druggability 0.85). MolNFT v1 #100100 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4MNG
- Type
- protein
- Length
- 1,200 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-2-microglobulin; CD1D1 protein; Tra@ PROTEIN,TRA@ protein, ti antigen CD3-associated…
- UniProt
- P01887, P15813, Q7TMK5, Q6PJ56
- Ligands
- CIS, NAG
- Pockets
- 9 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 13% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, D | Beta-2-microglobulin | protein | 99 | 0% helix, 52% strand | P01887 |
| A, C | CD1D1 protein | protein | 273 | 25% helix, 41% strand | P15813, Q7TMK5 |
| E, F | Tra@ PROTEIN,TRA@ protein, ti antigen CD3-associated protein gamma chain V-J-C region | protein | 228 | 3% helix, 50% strand | Q6PJ56 |
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 · 2 copies · chains A, E, C, F
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 740 | 0.85 | 0.88 | 69 | CIS |
| 2 | 747 | 0.84 | 0.87 | 66 | CIS |
| 3 | 923 | 0.77 | 0.80 | 74 | empty |
| 4 | 316 | 0.62 | 0.79 | 40 | empty |
| 5 | 126 | 0.45 | 0.78 | 26 | empty |
Interfaces
7 interfaces between chains.
- B–A · 1309 Ų buried · 15 hydrogen bonds · protein-protein
- D–C · 1303 Ų buried · 16 hydrogen bonds · protein-protein
- A–E · 634 Ų buried · 9 hydrogen bonds · protein-protein
- C–F · 620 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 426 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 4MNG · Structure of the DP10.7 TCR with CD1d-sulfatide · the same entry in another collection · chain F against F, TM-score 1.00
- P01887 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P01887) · a predicted model of the same protein · chain B against A, TM-score 0.98
- P15813 · AlphaFold monomer V2.0 prediction for antigen-presenting glycoprotein CD1D (P15813) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P01887
- Every structure of UniProt P15813
- Every structure of UniProt Q7TMK5
- Every structure of UniProt Q6PJ56
- Elsewhere: RCSB PDB 4MNG · PDBe 4MNG · UniProt P01887 · UniProt P15813 · UniProt Q7TMK5 · UniProt Q6PJ56
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