MolNFT v1 · #124159 · protein
Sidekick chimera containing sidekick-2 immunoglobulin domains 1-2 and sidekick-1 immunoglobulin domains 3-4
5K6Z · Protein sidekick-2,PROTEIN sidekick-1 chimera: “Sidekick chimera containing sidekick-2 immunoglobulin domains 1-2 and sidekick-1 immunoglobulin domains 3-4”. X-ray diffraction, 1 ligand (NAG), 5 pockets (best druggability 0.73).…
- PDB
- 5K6Z
- Type
- protein
- Length
- 753 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein sidekick-2,PROTEIN sidekick-1 chimera
- UniProt
- Q6V4S5, Q3UH53
- Ligands
- NAG
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein sidekick-2,PROTEIN sidekick-1 chimera | protein | 375 | 5% helix, 53% strand | Q6V4S5, Q3UH53 |
| B | Protein sidekick-2,PROTEIN sidekick-1 chimera | protein | 378 | 5% helix, 54% strand | Q6V4S5, Q3UH53 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains B, A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A, B
- CAC · Cacodylate ion · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 273 | 0.73 | 0.86 | 46 | CAC |
| 2 | 824 | 0.69 | 0.76 | 61 | empty |
| 3 | 169 | 0.59 | 0.82 | 20 | MPD |
| 4 | 128 | 0.55 | 0.82 | 18 | MPD |
| 5 | 123 | 0.40 | 0.75 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1419 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 5K6Z · Sidekick chimera containing sidekick-2 immunoglobulin domains 1-2 and sidekick-1… · the same entry in another collection · chain A against A, TM-score 1.00
- Q3UH53 · AlphaFold monomer V2.0 prediction for protein sidekick-1 (Q3UH53) · a predicted model of the same protein · chain A against A, TM-score 0.95
- Q6V4S5 · AlphaFold monomer V2.0 prediction for protein sidekick-2 (Q6V4S5) · a predicted model of the same protein · chain A against A, TM-score 0.92
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
- Every structure of UniProt Q3UH53
- Elsewhere: RCSB PDB 5K6Z · PDBe 5K6Z · UniProt Q6V4S5 · UniProt Q3UH53
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