MolNFT v1 · #85186 · protein
Crystal structure of the S. cerevisiae SKI2 insertion domain
4A4K · Antiviral helicase SKI2: “Crystal structure of the S. cerevisiae SKI2 insertion domain”. X-ray diffraction, 1 ligand (ZN), 12 pockets (best druggability 0.68). MolNFT v1 #85186 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 4A4K
- Type
- protein
- Length
- 1,226 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antiviral helicase SKI2
- EC
- 3.6.4.13
- UniProt
- P35207
- Ligands
- ZN
- Pockets
- 12 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G | Antiviral helicase SKI2 (EC 3.6.4.13) | protein | 246 | 45% helix, 17% strand | P35207 |
| C | Antiviral helicase SKI2 (EC 3.6.4.13) | protein | 245 | 46% helix, 18% strand | P35207 |
| E | Antiviral helicase SKI2 (EC 3.6.4.13) | protein | 244 | 45% helix, 18% strand | P35207 |
| I | Antiviral helicase SKI2 (EC 3.6.4.13) | protein | 245 | 45% helix, 18% strand | P35207 |
Ligands and binding sites
- ZN · Zinc ion · metal · 5 copies · chains A, C, E, G, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 601 | 0.68 | 0.77 | 71 | empty |
| 2 | 344 | 0.56 | 0.75 | 37 | empty |
| 3 | 353 | 0.55 | 0.74 | 37 | empty |
| 4 | 93 | 0.52 | 0.83 | 19 | empty |
| 5 | 101 | 0.51 | 0.82 | 28 | empty |
Interfaces
5 interfaces between chains.
- C–E · 506 Ų buried · 5 hydrogen bonds · protein-protein
- C–I · 482 Ų buried · 5 hydrogen bonds · protein-protein
- A–G · 481 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 462 Ų buried · 16 hydrogen bonds · protein-protein
- G–I · 461 Ų buried · 13 hydrogen bonds · protein-protein
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 P35207
- Elsewhere: RCSB PDB 4A4K · PDBe 4A4K · UniProt P35207
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