MolNFT v1 · #22215 · protein
N-terminal 3 domains of ci-mpr bound to mannose 6-phosphate
1SYO · Cation-independent mannose 6-phosphate receptor: “N-terminal 3 domains of ci-mpr bound to mannose 6-phosphate”. X-ray diffraction, 4 ligands (M6P, NAG, NDG), 7 pockets (best druggability 0.77). MolNFT v1 #22215 on GenesisL1: 3D…
- PDB
- 1SYO
- Type
- protein
- Length
- 830 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cation-independent mannose 6-phosphate receptor
- UniProt
- P08169
- Ligands
- M6P, NAG, NDG, BMA
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cation-independent mannose 6-phosphate receptor | protein | 422 | 11% helix, 43% strand | P08169 |
| B | Cation-independent mannose 6-phosphate receptor | protein | 408 | 8% helix, 43% strand | P08169 |
Ligands and binding sites
- M6P · 6-O-phosphono-alpha-D-mannopyranose · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · chains A
- BMA · beta-D-mannopyranose · sugar
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1000 | 0.77 | 0.79 | 82 | empty |
| 2 | 1031 | 0.76 | 0.79 | 78 | GOL |
| 3 | 127 | 0.42 | 0.75 | 17 | empty |
| 4 | 136 | 0.40 | 0.74 | 37 | M6P |
| 5 | 62 | 0.34 | 0.77 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 319 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 23 disulfide, 4 glycan (disulfide, glycosylation, N-glycosylation).
Compared structures
- 1SYO · N-terminal 3 domains of CI-MPR bound to mannose 6-phosphate · the same entry in another collection · chain A against A, TM-score 1.00
- P08169 · AlphaFold monomer V2.0 prediction for cation-independent mannose-6-phosphate receptor… · a predicted model of the same protein · chain A 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 P08169
- Elsewhere: RCSB PDB 1SYO · PDBe 1SYO · UniProt P08169
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