Research workbench
Structure of MCD1D with bound glycolipid bbgl-2F from borrelia burgdorferi
Analyse Structure of MCD1D with bound glycolipid bbgl-2F from borrelia burgdorferi in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ILP
- Type
- protein
- Length
- 365 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- T-cell surface glycoprotein CD1D1; Beta-2 microglobulin
- UniProt
- P11609, Q91XJ8
- Ligands
- 1L2, NAG
- Pockets
- 4 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 19% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | T-cell surface glycoprotein CD1D1 | protein | 266 | 27% helix, 43% strand | P11609 |
| B | Beta-2 microglobulin | protein | 99 | 0% helix, 49% strand | Q91XJ8 |
Ligands and binding sites
- 1L2 · (2S)-3-(alpha-D-galactopyranosyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl (9Z,12Z)-octadeca-9,12-dienoate · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A
- DMS · Dimethyl sulfoxide · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 618 | 0.85 | 0.89 | 59 | 1L2, DMS |
| 2 | 445 | 0.66 | 0.78 | 51 | empty |
| 3 | 123 | 0.46 | 0.78 | 25 | empty |
| 4 | 140 | 0.45 | 0.77 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1332 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 3ILP · Structure of mCD1d with bound glycolipid BbGL-2f from Borrelia burgdorferi · the same entry in another collection · chain A against A, TM-score 1.00
- P11609 · AlphaFold monomer V2.0 prediction for antigen-presenting glycoprotein CD1D1 (P11609) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P11609
- Every structure of UniProt Q91XJ8
- Elsewhere: RCSB PDB 3ILP · PDBe 3ILP · UniProt P11609 · UniProt Q91XJ8
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