Research workbench
Crystal structure cation-dependent mannose 6-phosphate receptor at pH 7.4
Analyse Crystal structure cation-dependent mannose 6-phosphate receptor at pH 7.4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CY4
- Type
- protein
- Length
- 305 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
- MAN, NAG
- Pockets
- 2 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cation-dependent mannose-6-phosphate receptor | protein | 151 | 13% helix, 44% strand | P11456 |
| B | Cation-dependent mannose-6-phosphate receptor | protein | 154 | 12% helix, 43% strand | P11456 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 6 copies
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 298 | 0.69 | 0.83 | 38 | empty |
| 2 | 73 | 0.32 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1101 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 glycan (disulfide, glycosylation).
Compared structures
- 3CY4 · Crystal Structure cation-dependent mannose 6-phosphate receptor at pH 7.4 · 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 B against A, TM-score 0.97
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 3CY4 · PDBe 3CY4 · UniProt P11456
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