Research workbench
Human cation-independent mannose 6-PHOSPHATE/IGF2 receptor domains 7- 11
Analyse Human cation-independent mannose 6-PHOSPHATE/IGF2 receptor domains 7- 11 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Z32
- Type
- protein
- Length
- 1,351 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cation-independent mannose-6-phosphate receptor
- UniProt
- P11717
- Ligands
- NAG, MAN, BMA, SO4
- Pockets
- 15 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cation-independent mannose-6-phosphate receptor | protein | 686 | 5% helix, 45% strand | P11717 |
| B | Cation-independent mannose-6-phosphate receptor | protein | 665 | 5% helix, 42% strand | P11717 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 6 copies · chains B, A
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 931 | 0.78 | 0.80 | 91 | empty |
| 2 | 1157 | 0.74 | 0.77 | 115 | empty |
| 3 | 520 | 0.67 | 0.78 | 63 | empty |
| 4 | 336 | 0.64 | 0.80 | 38 | empty |
| 5 | 273 | 0.56 | 0.77 | 37 | empty |
Interfaces
1 interface between chains.
- A–B · 3655 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 38 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 6Z32 · Human cation-independent mannose 6-phosphate/IGF2 receptor domains 7-11 · the same entry in another collection · chain B against B, TM-score 1.00
- P11717 · AlphaFold monomer V2.0 prediction for cation-independent mannose-6-phosphate receptor… · a predicted model of the same protein · chain B against A, TM-score 0.44
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 P11717
- Elsewhere: RCSB PDB 6Z32 · PDBe 6Z32 · UniProt P11717
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