MolNFT v1 · #18862 · protein
Crystal structure of N-terminal 3 domains of ci-mpr
1Q25 · Cation-independent mannose 6-phosphate receptor: “Crystal structure of N-terminal 3 domains of ci-mpr”. X-ray diffraction, 3 ligands (NAG, MAN, BMA), 3 pockets (best druggability 0.78). MolNFT v1 #18862 on GenesisL1: 3D structure…
- PDB
- 1Q25
- Type
- protein
- Length
- 428 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cation-independent mannose 6-phosphate receptor
- UniProt
- P08169
- Ligands
- NAG, MAN, BMA
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 9% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cation-independent mannose 6-phosphate receptor | protein | 428 | 9% helix, 42% strand | P08169 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · 2 copies
- BMA · beta-D-mannopyranose · sugar
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 976 | 0.78 | 0.80 | 68 | empty |
| 2 | 104 | 0.40 | 0.76 | 14 | empty |
| 3 | 52 | 0.25 | 0.73 | 17 | empty |
Modifications
Observed in the structure: 12 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 1Q25 · Crystal structure of N-terminal 3 domains of CI-MPR · 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 0.96
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 P08169
- Elsewhere: RCSB PDB 1Q25 · PDBe 1Q25 · UniProt P08169
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