MolNFT v1 · #125218 · protein
Crystal structure of human CD1B in complex with C36-gmm
5L2J · T-cell surface glycoprotein CD1B: “Crystal structure of human CD1B in complex with C36-gmm”. X-ray diffraction, 8 ligands (6UL, 70E, NAG), 6 pockets (best druggability 0.86). MolNFT v1 #125218 on GenesisL1: 3D structure, binding…
- PDB
- 5L2J
- Type
- protein
- Length
- 377 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
- 6UL, 70E, NAG, MAN, FUC, BMA, NA, CL
- Pockets
- 6 · best druggability 0.86
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 | 97 | 0% helix, 51% strand | P61769 |
Ligands and binding sites
- 6UL · Tetracosyl palmitate · ligand · chains A
- 70E · 6-O-[(2R,3R)-3-hydroxy-2-tetradecyldocosanoyl]-alpha-L-idopyranose · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · 2 copies
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A
- BMA · beta-D-mannopyranose · sugar
- NA · Sodium ion · metal · chains B
- CL · Chloride ion · ion · 2 copies · chains A
- ACT · Acetate ion · additive · 2 copies · 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 | 686 | 0.86 | 0.90 | 64 | 6UL, 70E |
| 2 | 372 | 0.63 | 0.78 | 43 | empty |
| 3 | 134 | 0.42 | 0.75 | 24 | ACT |
| 4 | 114 | 0.40 | 0.76 | 26 | empty |
| 5 | 80 | 0.35 | 0.76 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1187 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 5L2J · Crystal Structure of human CD1b in complex with C36-GMM · the same entry in another collection · chain A against A, 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 0.99
- 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
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 5L2J · PDBe 5L2J · UniProt P29016 · UniProt P61769
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