MolNFT v1 · #50537 · protein
Crystal structure cation-dependent mannose 6-phosphate receptor at pH 4.8
2RL7 · Cation-dependent mannose-6-phosphate receptor: “Crystal structure cation-dependent mannose 6-phosphate receptor at pH 4.8”. X-ray diffraction, 1 ligand (NAG), 6 pockets (best druggability 0.71). MolNFT v1 #50537 on GenesisL1: 3D…
- PDB
- 2RL7
- Type
- protein
- Length
- 594 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cation-dependent mannose-6-phosphate receptor
- UniProt
- P11456
- Ligands
- NAG
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cation-dependent mannose-6-phosphate receptor | protein | 148 | 8% helix, 52% strand | P11456 |
| B, C | Cation-dependent mannose-6-phosphate receptor | protein | 147 | 10% helix, 52% strand | P11456 |
| D | Cation-dependent mannose-6-phosphate receptor | protein | 152 | 10% helix, 47% strand | P11456 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 5 copies · chains B, C, D
- GOL · Glycerol · additive · 2 copies · chains A, C
- CAC · Cacodylate ion · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 569 | 0.71 | 0.79 | 54 | empty |
| 2 | 144 | 0.63 | 0.85 | 32 | empty |
| 3 | 132 | 0.56 | 0.83 | 28 | empty |
| 4 | 98 | 0.39 | 0.76 | 18 | empty |
| 5 | 97 | 0.35 | 0.74 | 15 | empty |
Interfaces
4 interfaces between chains.
- C–D · 865 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 821 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 183 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 151 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 2RL7 · Crystal Structure cation-dependent mannose 6-phosphate receptor at pH 4.8 · 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 D 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 2RL7 · PDBe 2RL7 · UniProt P11456
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.