MolNFT v1 · #152025 · protein
Long wavelength native-sad phasing of SEN1 helicase
6I59 · Helicase SEN1: “Long wavelength native-sad phasing of SEN1 helicase”. X-ray diffraction, 2 ligands (ADP, MG), 12 pockets (best druggability 0.55). MolNFT v1 #152025 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6I59
- Type
- protein
- Length
- 682 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Helicase SEN1
- EC
- 3.6.4.-
- UniProt
- Q00416
- Ligands
- ADP, MG
- Pockets
- 12 · best druggability 0.55
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Helicase SEN1 (EC 3.6.4.-) | protein | 682 | 42% helix, 19% strand | Q00416 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- MG · Magnesium ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 40 copies · chains A
- GOL · Glycerol · additive · 12 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · 11 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 294 | 0.55 | 0.76 | 29 | GOL |
| 2 | 61 | 0.52 | 0.86 | 16 | empty |
| 3 | 222 | 0.51 | 0.76 | 29 | EDO, PEG, MG |
| 4 | 130 | 0.45 | 0.77 | 26 | EDO |
| 5 | 137 | 0.40 | 0.74 | 19 | empty |
Modifications
Observed in the structure: 1 covalent (additive adduct).
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 Q00416
- Elsewhere: RCSB PDB 6I59 · PDBe 6I59 · UniProt Q00416
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