MolNFT v1 · #78347 · protein
Structure of human CD1E
3S6C · Beta-2-microglobulin, T-cell surface glycoprotein CD1E…: “Structure of human CD1E”. X-ray diffraction, 2 ligands (NAG, FUC), 6 pockets (best druggability 0.83). MolNFT v1 #78347 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 3S6C
- Type
- protein
- Length
- 372 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-2-microglobulin, T-cell surface glycoprotein CD1E, membrane-associated
- UniProt
- P61769, P15812
- Ligands
- NAG, FUC
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 19% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-2-microglobulin, T-cell surface glycoprotein CD1E, membrane-associated | protein | 372 | 19% helix, 35% strand | P61769, P15812 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- FUC · alpha-L-fucopyranose · sugar · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 722 | 0.83 | 0.86 | 58 | empty |
| 2 | 440 | 0.66 | 0.78 | 48 | empty |
| 3 | 74 | 0.49 | 0.83 | 17 | empty |
| 4 | 133 | 0.44 | 0.77 | 27 | empty |
| 5 | 75 | 0.37 | 0.77 | 17 | empty |
Modifications
Observed in the structure: 3 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 3S6C · Structure of human CD1e · the same entry in another collection · chain A against A, TM-score 1.00
- P15812 · AlphaFold monomer V2.0 prediction for T-cell surface glycoprotein CD1E… · a predicted model of the same protein · chain A against A, TM-score 0.71
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain A against A, TM-score 0.26
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 P61769
- Every structure of UniProt P15812
- Elsewhere: RCSB PDB 3S6C · PDBe 3S6C · UniProt P61769 · UniProt P15812
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