MolNFT v1 · #118242 · protein
Structure of ligand binding region of uparap at pH 7.4 without calcium
5EW6 · C-type mannose receptor 2: “Structure of ligand binding region of uparap at pH 7.4 without calcium”. X-ray diffraction, 2 ligands (NAG, NA), 1 pocket (best druggability 0.62). MolNFT v1 #118242 on GenesisL1: 3D structure, binding…
- 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
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