Research workbench
CD1A-42:2 sm binary complex
Analyse CD1A-42:2 sm binary complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KP1
- Type
- protein
- Length
- 378 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
- FO4
- Pockets
- 5 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 20% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | T-cell surface glycoprotein CD1A | protein | 274 | 28% helix, 41% strand | P06126 |
| B | Beta-2-microglobulin | protein | 104 | 0% helix, 47% strand | P61769 |
Ligands and binding sites
- FO4 · sphingomyelin · ligand · chains A
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A, B
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 | 765 | 0.84 | 0.86 | 52 | FO4 |
| 2 | 365 | 0.61 | 0.77 | 42 | empty |
| 3 | 82 | 0.39 | 0.78 | 22 | empty |
| 4 | 102 | 0.39 | 0.76 | 24 | empty |
| 5 | 68 | 0.33 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1397 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7KP1 · CD1a-42:2 SM binary complex · 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 0.96
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain B against A, TM-score 0.91
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 7KP1 · PDBe 7KP1 · UniProt P06126 · UniProt P61769
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