Research workbench
CD1C with antigen analogue 2
Analyse CD1C with antigen analogue 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MXF
- Type
- protein
- Length
- 380 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- T-cell surface glycoprotein CD1C, T-cell surface glycoprotein CD1B chimeric protein…
- UniProt
- P29017, P29016, P61769
- Ligands
- ZQ4, D12, ZP7, NAG
- Pockets
- 6 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 18% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | T-cell surface glycoprotein CD1C, T-cell surface glycoprotein CD1B chimeric protein | protein | 276 | 25% helix, 42% strand | P29017, P29016 |
| B | Beta-2-microglobulin | protein | 104 | 0% helix, 50% strand | P61769 |
Ligands and binding sites
- ZQ4 · 2,6-anhydro-1-deoxy-1-[(S)-hydroxy{[(4r,8s,12r,16r, 20S)-4,8,12,16,20-pentamethylheptacosyl]oxy}phosphoryl]-D-glycero-D-galacto-heptitol · ligand · chains A
- D12 · Dodecane · ligand · chains A
- ZP7 · (2S)-2,3-dihydroxypropyl hexadecanoate · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- NHE · 2-[N-cyclohexylamino]ethane sulfonic acid · additive · chains A, B
- MLA · Malonic acid · additive · chains A, B
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 | 640 | 0.85 | 0.89 | 59 | ZQ4, D12, ZP7 |
| 2 | 306 | 0.66 | 0.81 | 31 | NHE, MLA |
| 3 | 104 | 0.38 | 0.75 | 15 | empty |
| 4 | 88 | 0.35 | 0.75 | 23 | empty |
| 5 | 59 | 0.32 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1550 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7MXF · CD1c with antigen analogue 2 · the same entry in another collection · chain A against A, TM-score 1.00
- P29017 · AlphaFold monomer V2.0 prediction for T-cell surface glycoprotein CD1C (P29017) · 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 0.93
- P29016 · AlphaFold monomer V2.0 prediction for T-cell surface glycoprotein CD1B (P29016) · a predicted model of the same protein · chain A against A, TM-score 0.92
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 P29017
- Every structure of UniProt P29016
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 7MXF · PDBe 7MXF · UniProt P29017 · UniProt P29016 · UniProt P61769
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