MolNFT v1 · #152816 · protein + DNA
Structure of helicobacter pylori soj-ADP complex bound to DNA
6IUD · Spooj regulator (soj): “Structure of helicobacter pylori soj-ADP complex bound to DNA”. X-ray diffraction, 2 ligands (ADP, MG), 7 pockets (best druggability 0.90). MolNFT v1 #152816 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6IUD
- 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
- ADP, MG
- Pockets
- 7 · 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
- ADP · Adenosine-5'-diphosphate · 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
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1074 | 0.90 | 0.92 | 131 | ADP, MG |
| 2 | 1094 | 0.88 | 0.89 | 109 | ADP, MG |
| 3 | 471 | 0.74 | 0.83 | 54 | empty |
| 4 | 63 | 0.56 | 0.89 | 23 | empty |
| 5 | 92 | 0.36 | 0.75 | 18 | empty |
Interfaces
11 interfaces between chains.
- C–D · 1464 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1458 Ų buried · 8 hydrogen bonds · protein-protein
- E–F · 1064 Ų buried · 93 hydrogen bonds · nucleic-nucleic
- A–F · 170 Ų buried · 1 hydrogen bond · protein-nucleic
- D–E · 170 Ų buried · 2 hydrogen bonds · protein-nucleic
Compared structures
- 6IUD · Structure of Helicobacter pylori Soj-ADP 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 6IUD · PDBe 6IUD · UniProt O25759
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