MolNFT v1 · #125663 · protein
Crystal structure of glycosylated myelin-associated glycoprotein (mag) IG1-3
5LFR: “Crystal structure of glycosylated myelin-associated glycoprotein (mag) IG1-3”. X-ray diffraction, 4 ligands (NAG, MAN, BMA), 5 pockets (best druggability 0.69). MolNFT v1 #125663 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5LFR
- Type
- protein
- Length
- 622 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Myelin-associated glycoprotein
- UniProt
- P20917
- Ligands
- NAG, MAN, BMA, SO4
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Myelin-associated glycoprotein | protein | 310 | 7% helix, 54% strand | P20917 |
| B | Myelin-associated glycoprotein | protein | 312 | 4% helix, 54% strand | P20917 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 5 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
- GOL · Glycerol · additive · 4 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 440 | 0.69 | 0.80 | 38 | NAG |
| 2 | 457 | 0.66 | 0.78 | 43 | NAG |
| 3 | 302 | 0.57 | 0.76 | 27 | SO4 |
| 4 | 55 | 0.32 | 0.77 | 14 | empty |
| 5 | 68 | 0.32 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1504 Ų buried · 29 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 glycan, 8 disulfide (disulfide, N-glycosylation, C-mannosylation).
Compared structures
- 5LFR · Crystal structure of glycosylated Myelin-associated glycoprotein (MAG) Ig1-3 · the same entry in another collection · chain A against A, TM-score 1.00
- P20917 · AlphaFold monomer V2.0 prediction for myelin-associated glycoprotein (P20917) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P20917
- Elsewhere: RCSB PDB 5LFR · PDBe 5LFR · UniProt P20917
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