Research workbench
Crystal structure of scd-mpr mutant E19Q/K137M bound to man-6-P
Analyse Crystal structure of scd-mpr mutant E19Q/K137M bound to man-6-P in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3K41
- Type
- protein
- Length
- 296 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cation-dependent mannose-6-phosphate receptor
- UniProt
- P11456
- Ligands
- M6D, NAG, BMA, MAN
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 14% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cation-dependent mannose-6-phosphate receptor | protein | 145 | 13% helix, 45% strand | P11456 |
| B | Cation-dependent mannose-6-phosphate receptor | protein | 151 | 14% helix, 44% strand | P11456 |
Ligands and binding sites
- M6D · 6-O-phosphono-beta-D-mannopyranose · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar
- MAN · alpha-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 60 | 0.73 | 0.98 | 15 | empty |
| 2 | 191 | 0.51 | 0.77 | 33 | M6D |
| 3 | 107 | 0.40 | 0.76 | 18 | empty |
| 4 | 57 | 0.34 | 0.78 | 13 | empty |
| 5 | 85 | 0.34 | 0.74 | 21 | M6D |
Interfaces
1 interface between chains.
- A–B · 1138 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 3K41 · Crystal structure of sCD-MPR mutant E19Q/K137M bound to Man-6-P · the same entry in another collection · chain A against A, TM-score 1.00
- P11456 · AlphaFold monomer V2.0 prediction for cation-dependent 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 P11456
- Elsewhere: RCSB PDB 3K41 · PDBe 3K41 · UniProt P11456
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