Research workbench
N-terminal 3 domains of ci-mpr bound to mannose 6-phosphate
Analyse N-terminal 3 domains of ci-mpr bound to mannose 6-phosphate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1SZ0
- Type
- protein
- Length
- 833 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, OS
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cation-independent mannose 6-phosphate receptor | protein | 417 | 8% helix, 41% strand | P08169 |
| B | Cation-independent mannose 6-phosphate receptor | protein | 416 | 10% helix, 42% 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 · 6 copies · chains B, A
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · chains A
- OS · Osmium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 991 | 0.77 | 0.79 | 84 | empty |
| 2 | 1004 | 0.77 | 0.79 | 74 | empty |
| 3 | 205 | 0.47 | 0.75 | 38 | M6P |
| 4 | 119 | 0.41 | 0.75 | 14 | empty |
| 5 | 75 | 0.32 | 0.74 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 345 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 24 disulfide, 4 glycan (disulfide, glycosylation, N-glycosylation).
Compared structures
- 1SZ0 · 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 1SZ0 · PDBe 1SZ0 · UniProt P08169
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