Research workbench
Gadolinium mri contrast compound binding in human plasma glycoprotein afamin - resurrection of highly anisotropic data
Analyse Gadolinium mri contrast compound binding in human plasma glycoprotein afamin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RQ7
- Type
- protein
- Length
- 479 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Afamin
- UniProt
- P43652
- Ligands
- DO3, NAG, GD
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 64% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Afamin | protein | 479 | 64% helix, 0% strand | P43652 |
Ligands and binding sites
- DO3 · 10-((2R)-2-hydroxypropyl)-1,4,7,10-tetraazacyclododecane 1,4,7-triacetic acid · ligand · 3 copies · chains B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains B
- GD · Gadolinium atom · metal · 3 copies
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 | 1010 | 0.79 | 0.80 | 98 | GD, DO3 |
| 2 | 122 | 0.54 | 0.82 | 23 | empty |
| 3 | 89 | 0.50 | 0.83 | 16 | empty |
| 4 | 54 | 0.47 | 0.85 | 14 | empty |
| 5 | 71 | 0.43 | 0.80 | 15 | empty |
Modifications
Observed in the structure: 13 disulfide, 3 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 P43652
- Elsewhere: RCSB PDB 6RQ7 · PDBe 6RQ7 · UniProt P43652
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