MolNFT v1 · #12365 · protein
Twists and turns of the CD-mpr: ligand-bound versus ligand-free receptor
1KEO · Cation-dependent mannose-6-phosphate receptor: “Twists and turns of the CD-mpr: ligand-bound versus ligand-free receptor”. X-ray diffraction, 1 ligand (NAG), 5 pockets (best druggability 0.64). MolNFT v1 #12365 on GenesisL1: 3D…
- PDB
- 1KEO
- Type
- protein
- Length
- 304 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
- NAG
- Pockets
- 5 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 10% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cation-dependent mannose-6-phosphate receptor | protein | 152 | 10% helix, 51% strand | P11456 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 111 | 0.64 | 0.88 | 25 | empty |
| 2 | 168 | 0.46 | 0.76 | 26 | empty |
| 3 | 134 | 0.41 | 0.75 | 27 | empty |
| 4 | 83 | 0.35 | 0.76 | 15 | empty |
| 5 | 55 | 0.29 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 860 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 1KEO · Twists and turns of the CD-mpr: ligand-bound versus ligand-free receptor · 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 0.94
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 1KEO · PDBe 1KEO · UniProt P11456
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