Research workbench
Crystal structure of CD1A in complex with a synthetic mycobactin lipopeptide
Analyse Crystal structure of CD1A in complex with a synthetic mycobactin lipopeptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XZ0
- Type
- protein
- Length
- 737 residues
- Chains
- 4
- 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
- JH0, NAG, FUC
- Pockets
- 11 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 26% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | T-cell surface glycoprotein CD1A | protein | 271 | 31% helix, 42% strand | P06126 |
| B, D | Beta-2-microglobulin | protein | 98 | 0% helix, 52% strand | P61769 |
| C | T-cell surface glycoprotein CD1A | protein | 270 | 31% helix, 43% strand | P06126 |
Ligands and binding sites
- JH0 · 6-(hydroxy-hexadecanoyl-amino)-2-{[(4S)-2-(2-hydroxy-phenyl)-4,5-dihydro-oxazole-4-carbonyl]-amino}-hexanoic acid 2-[(3S)-1-(tert-butyl-diphenyl-silanyloxy)-2-oxo-azepan-3-ylcarbamoyl]-(1S)-1-methyl-ethyl ester · ligand · 2 copies · chains A, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, C
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 720 | 0.85 | 0.88 | 48 | JH0 |
| 2 | 711 | 0.84 | 0.87 | 50 | JH0 |
| 3 | 603 | 0.67 | 0.76 | 56 | empty |
| 4 | 416 | 0.64 | 0.78 | 41 | empty |
| 5 | 270 | 0.56 | 0.77 | 39 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1271 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1267 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 201 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 1XZ0 · Crystal structure of CD1a in complex with a synthetic mycobactin lipopeptide · the same entry in another collection · chain D against D, TM-score 1.00
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain B against A, TM-score 0.97
- 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
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 1XZ0 · PDBe 1XZ0 · UniProt P06126 · UniProt P61769
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