Research workbench
Structure of ligand binding region of uparap at pH 7.4
Analyse Structure of ligand binding region of uparap at pH 7.4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5E4K
- Type
- protein
- Length
- 424 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, CA, NA
- Pockets
- 4 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain · 14% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | C-type mannose receptor 2 | protein | 424 | 14% helix, 34% strand | Q9UBG0 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- CA · Calcium ion · metal · 2 copies · chains A
- NA · Sodium ion · metal · chains A
- 1PE · Pentaethylene glycol · additive · chains A
- PE5 · 3,6,9,12,15,18,21,24-octaoxahexacosan-1-ol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 322 | 0.61 | 0.78 | 30 | empty |
| 2 | 86 | 0.41 | 0.78 | 19 | empty |
| 3 | 109 | 0.40 | 0.76 | 26 | empty |
| 4 | 70 | 0.32 | 0.75 | 15 | empty |
Modifications
Observed in the structure: 11 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
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 5E4K · PDBe 5E4K · UniProt Q9UBG0
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