Research workbench
CD1A binary complex with sphingomyelin
Analyse CD1A binary complex with sphingomyelin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4X6F
- Type
- protein
- Length
- 361 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- T-cell surface glycoprotein CD1A; Beta-2-microglobulin
- UniProt
- P06126, P61769
- Ligands
- 3XU
- Pockets
- 5 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | T-cell surface glycoprotein CD1A | protein | 263 | 33% helix, 40% strand | P06126 |
| B | Beta-2-microglobulin | protein | 98 | 0% helix, 50% strand | P61769 |
Ligands and binding sites
- 3XU · (4S,7S,23Z)-4-hydroxy-7-[(1S,2Z)-1-hydroxyhexadec-2-en-1-yl]-N,N,N-trimethyl-9-oxo-3,5-dioxa-8-aza-4-phosphadotriacont- 23-en-1-aminium 4-oxide · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 604 | 0.86 | 0.91 | 48 | 3XU |
| 2 | 436 | 0.64 | 0.77 | 49 | empty |
| 3 | 140 | 0.45 | 0.77 | 33 | empty |
| 4 | 88 | 0.34 | 0.75 | 24 | empty |
| 5 | 51 | 0.30 | 0.77 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1356 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 4X6F · CD1a binary complex with sphingomyelin · the same entry in another collection · chain A against A, 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 0.96
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
- Elsewhere: RCSB PDB 4X6F · PDBe 4X6F · UniProt P06126 · UniProt P61769
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