Research workbench
Structure of helicobacter pylori soj-ATP complex bound to DNA
Analyse Structure of helicobacter pylori soj-ATP complex bound to DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6IUC
- Type
- protein + DNA
- Length
- 1,104 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spooj regulator (soj); DNA (5'- D(P*TP*CP*CP*CP*TP*GP*TP*TP*TP*CP*AP*CP*GP*TP*GP*GP*AP*AP*…
- UniProt
- O25759
- Ligands
- ATP, MG
- Pockets
- 8 · best druggability 0.90
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Spooj regulator (soj) | protein | 264 | 47% helix, 16% strand | O25759 |
| E | DNA (5'- D(P*TP*CP*CP*CP*TP*GP*TP*TP*TP*CP*AP*CP*GP*TP*GP*GP*AP*AP*CP*AP*CP*CP *CP*T)-3') | dna | 24 | — | — |
| F | DNA (5'- D(P*AP*GP*GP*GP*TP*GP*TP*TP*CP*CP*AP*CP*GP*TP*GP*AP*AP*AP*CP*AP*GP*GP *GP*A)-3') | dna | 24 | — | — |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1161 | 0.90 | 0.91 | 135 | ATP |
| 2 | 1117 | 0.89 | 0.91 | 117 | ATP, MG |
| 3 | 236 | 0.45 | 0.73 | 21 | empty |
| 4 | 104 | 0.38 | 0.76 | 17 | empty |
| 5 | 72 | 0.32 | 0.74 | 14 | empty |
Interfaces
11 interfaces between chains.
- C–D · 1528 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1515 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 1049 Ų buried · 91 hydrogen bonds · nucleic-nucleic
- A–E · 168 Ų buried · 1 hydrogen bond · protein-nucleic
- C–F · 166 Ų buried · 1 hydrogen bond · protein-nucleic
Compared structures
- 6IUC · Structure of Helicobacter pylori Soj-ATP complex bound to DNA · the same entry in another collection · chain A against A, TM-score 1.00
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 O25759
- Elsewhere: RCSB PDB 6IUC · PDBe 6IUC · UniProt O25759
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