Research workbench
Crystal structure of human CD1D-lysophosphatidylcholine
Analyse Crystal structure of human CD1D-lysophosphatidylcholine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3U0P
- Type
- protein
- Length
- 1,056 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antigen-presenting glycoprotein CD1D; Beta-2-microglobulin
- UniProt
- P15813, P61769
- Ligands
- LSC, NBU, FUC, NAG, SO4
- Pockets
- 16 · best druggability 0.87
Structure
x-ray diffraction · 6 distinct chains · 20% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Antigen-presenting glycoprotein CD1D | protein | 273 | 28% helix, 39% strand | P15813 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 52% strand | P61769 |
| C | Antigen-presenting glycoprotein CD1D | protein | 274 | 25% helix, 39% strand | P15813 |
| D | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| E | Antigen-presenting glycoprotein CD1D | protein | 228 | 29% helix, 31% strand | P15813 |
| F | Beta-2-microglobulin | protein | 82 | 0% helix, 33% strand | P61769 |
Ligands and binding sites
- LSC · (4R,7R,18E)-4,7-dihydroxy-N,N,N-trimethyl-10-oxo-3,5,9-trioxa-4-phosphaheptacos-18-en-1-aminium 4-oxide · ligand · 2 copies · chains A, C
- NBU · N-butane · ligand · chains A, E
- FUC · alpha-L-fucopyranose · sugar · 5 copies · chains A, B, C, D, E, F
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, C, E
- SO4 · Sulfate ion · ion · 11 copies · chains A, C, D, F
- GOL · Glycerol · additive · 7 copies · chains A, B, C, D
- HEX · Hexane · additive · chains A
- UND · Undecane · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 741 | 0.87 | 0.90 | 69 | NBU |
| 2 | 735 | 0.86 | 0.89 | 62 | LSC |
| 3 | 737 | 0.84 | 0.87 | 58 | LSC, HEX, UND |
| 4 | 462 | 0.66 | 0.78 | 58 | GOL |
| 5 | 210 | 0.65 | 0.84 | 30 | empty |
Interfaces
7 interfaces between chains.
- C–D · 1412 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1354 Ų buried · 22 hydrogen bonds · protein-protein
- E–F · 1180 Ų buried · 18 hydrogen bonds · protein-protein
- C–E · 513 Ų buried · 10 hydrogen bonds · protein-protein
- A–E · 472 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 3U0P · Crystal structure of human CD1d-lysophosphatidylcholine · the same entry in another collection · chain F against F, TM-score 1.00
- P15813 · AlphaFold monomer V2.0 prediction for antigen-presenting glycoprotein CD1D (P15813) · a predicted model of the same protein · chain E against A, TM-score 0.99
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain D 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 P15813
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 3U0P · PDBe 3U0P · UniProt P15813 · UniProt P61769
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