Research workbench
Sidekick-2 immunoglobulin domains 1-4 H18R/N22S mutant
Analyse Sidekick-2 immunoglobulin domains 1-4 H18R/N22S mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5K70
- Type
- protein
- Length
- 1,495 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein sidekick-2
- UniProt
- Q6V4S5
- Ligands
- NAG, FUC, PO4
- Pockets
- 12 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 4% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein sidekick-2 | protein | 381 | 4% helix, 52% strand | Q6V4S5 |
| B | Protein sidekick-2 | protein | 377 | 4% helix, 53% strand | Q6V4S5 |
| C | Protein sidekick-2 | protein | 374 | 4% helix, 51% strand | Q6V4S5 |
| D | Protein sidekick-2 | protein | 363 | 3% helix, 52% strand | Q6V4S5 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B, C, D
- FUC · alpha-L-fucopyranose · sugar · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 14 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 831 | 0.74 | 0.79 | 93 | empty |
| 2 | 889 | 0.74 | 0.78 | 90 | empty |
| 3 | 685 | 0.69 | 0.77 | 58 | empty |
| 4 | 108 | 0.52 | 0.82 | 22 | empty |
| 5 | 92 | 0.45 | 0.80 | 14 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1723 Ų buried · 32 hydrogen bonds · protein-protein
- C–D · 1693 Ų buried · 28 hydrogen bonds · protein-protein
- B–D · 1058 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 53 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 47 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 7 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 Q6V4S5
- Elsewhere: RCSB PDB 5K70 · PDBe 5K70 · UniProt Q6V4S5
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