Research workbench
Crystal structure of human CD1B in complex with popc
Analyse Crystal structure of human CD1B in complex with popc in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6D64
- Type
- protein
- Length
- 382 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- T-cell surface glycoprotein CD1B; Beta-2-microglobulin
- UniProt
- P29016, P61769
- Ligands
- POV, CUY, NAG, MAN, FUC, BMA, NA, CL, IOD
- Pockets
- 5 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 19% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | T-cell surface glycoprotein CD1B | protein | 282 | 26% helix, 41% strand | P29016 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
Ligands and binding sites
- POV · (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate · ligand · chains A
- CUY · tetracosyl octadecanoate · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · 4 copies
- FUC · alpha-L-fucopyranose · sugar · 4 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 2 copies
- NA · Sodium ion · metal · chains A
- CL · Chloride ion · ion · 7 copies · chains A, B
- IOD · Iodide ion · ion · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · 3 copies · 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 | 827 | 0.87 | 0.90 | 73 | POV, CUY |
| 2 | 291 | 0.62 | 0.80 | 36 | empty |
| 3 | 166 | 0.46 | 0.76 | 34 | EDO |
| 4 | 182 | 0.46 | 0.75 | 34 | CL |
| 5 | 69 | 0.28 | 0.73 | 14 | CL |
Interfaces
1 interface between chains.
- A–B · 1372 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 6D64 · Crystal Structure of Human CD1b in Complex with POPC · the same entry in another collection · chain A against A, TM-score 1.00
- 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 0.97
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 P29016
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 6D64 · PDBe 6D64 · UniProt P29016 · UniProt P61769
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