Research workbench
Crystal structure of mouse md-1 in complex with phosphatidylcholine
Analyse Crystal structure of mouse md-1 in complex with phosphatidylcholine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3M7O
- Type
- protein
- Length
- 530 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lymphocyte antigen 86
- UniProt
- O88188
- Ligands
- BEN, L9R, NAG
- Pockets
- 3 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 0% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lymphocyte antigen 86 | protein | 137 | 0% helix, 59% strand | O88188 |
| B, C, D | Lymphocyte antigen 86 | protein | 131 | 0% helix, 56% strand | O88188 |
Ligands and binding sites
- BEN · Benzamidine · ligand · 16 copies · chains A, D, B, C
- L9R · (2S)-3-(octadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate · ligand · 2 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1062 | 0.88 | 0.88 | 87 | L9R |
| 2 | 1043 | 0.88 | 0.88 | 90 | L9R |
| 3 | 1178 | 0.78 | 0.80 | 121 | NAG, BEN |
Interfaces
5 interfaces between chains.
- C–D · 525 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 490 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 252 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 188 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 179 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 12 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 3M7O · Crystal structure of mouse MD-1 in complex with phosphatidylcholine · the same entry in another collection · chain A against A, TM-score 1.00
- O88188 · AlphaFold monomer V2.0 prediction for lymphocyte antigen 86 (O88188) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 O88188
- Elsewhere: RCSB PDB 3M7O · PDBe 3M7O · UniProt O88188
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