Research workbench
Structure of ligand binding region of uparap at pH 7.4 without calcium
Analyse Structure of ligand binding region of uparap at pH 7.4 without calcium in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EW6
- Type
- protein
- Length
- 442 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- C-type mannose receptor 2
- UniProt
- Q9UBG0
- Ligands
- NAG, NA
- Pockets
- 1 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 13% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | C-type mannose receptor 2 | protein | 442 | 13% helix, 33% strand | Q9UBG0 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
- NA · Sodium ion · metal · 2 copies · chains A
- 1PE · Pentaethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 321 | 0.62 | 0.79 | 31 | empty |
Modifications
Observed in the structure: 11 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 5EW6 · Structure of ligand binding region of uPARAP at pH 7.4 without calcium · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UBG0 · AlphaFold monomer V2.0 prediction for C-type mannose receptor 2 (Q9UBG0) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q9UBG0
- Elsewhere: RCSB PDB 5EW6 · PDBe 5EW6 · UniProt Q9UBG0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.