MolNFT v1 · #138496 · protein
Crystal structure of human CD1B in complex with pg
5WL1 · T-cell surface glycoprotein CD1B: “Crystal structure of human CD1B in complex with pg”. X-ray diffraction, 9 ligands (CUY, D3D, NAG), 5 pockets (best druggability 0.87). MolNFT v1 #138496 on GenesisL1: 3D structure, binding sites…
- PDB
- 5WL1
- Type
- protein
- Length
- 378 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
- CUY, D3D, NAG, FUC, MAN, BMA, NA, IOD, CL
- Pockets
- 5 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 19% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | T-cell surface glycoprotein CD1B | protein | 280 | 26% helix, 42% strand | P29016 |
| B | Beta-2-microglobulin | protein | 98 | 0% helix, 50% strand | P61769 |
Ligands and binding sites
- CUY · tetracosyl octadecanoate · ligand · chains A
- D3D · (19S,22R,25R)-22,25,26-trihydroxy-16,22-dioxo-17,21,23-trioxa-22lambda~5~-phosphahexacosan-19-yl (9E)-octadec-9-enoate · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A
- FUC · alpha-L-fucopyranose · sugar · 5 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 3 copies
- BMA · beta-D-mannopyranose · sugar · 2 copies
- NA · Sodium ion · metal · 2 copies · chains A, B
- IOD · Iodide ion · ion · chains A
- CL · Chloride ion · ion · 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 | 799 | 0.87 | 0.90 | 72 | CUY, D3D |
| 2 | 326 | 0.65 | 0.80 | 37 | NA |
| 3 | 130 | 0.44 | 0.77 | 28 | EDO |
| 4 | 114 | 0.35 | 0.73 | 24 | empty |
| 5 | 70 | 0.28 | 0.72 | 14 | CL |
Interfaces
1 interface between chains.
- A–B · 1259 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 5WL1 · Crystal Structure of Human CD1b in Complex with PG · 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 0.98
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 5WL1 · PDBe 5WL1 · UniProt P29016 · UniProt P61769
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