Research workbench
Structure of sulfolobus solfataricus sega-ADP complex bound to DNA
Analyse Structure of sulfolobus solfataricus sega-ADP 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
- 7DWR
- Type
- protein + DNA
- Length
- 976 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Soj protein (soj); DNA (5'- D(P*AP*GP*GP*GP*TP*GP*TP*TP*CP*CP*AP*CP*GP*TP*GP*AP*AP*AP*CP*A…
- UniProt
- Q981B3
- Ligands
- ADP, MG
- Pockets
- 7 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Soj protein (soj) | protein | 220 | 42% helix, 19% strand | Q981B3 |
| E, G | 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 | — | — |
| F, H | 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 | — | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, F, B, H, 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 285 | 0.61 | 0.79 | 40 | ADP, MG |
| 2 | 324 | 0.59 | 0.78 | 38 | ADP, MG |
| 3 | 421 | 0.55 | 0.73 | 29 | empty |
| 4 | 159 | 0.47 | 0.77 | 34 | ADP, MG |
| 5 | 122 | 0.47 | 0.78 | 31 | ADP, MG |
Interfaces
10 interfaces between chains.
- E–F · 1159 Ų buried · 81 hydrogen bonds · nucleic-nucleic
- G–H · 1116 Ų buried · 111 hydrogen bonds · nucleic-nucleic
- A–C · 869 Ų buried · 8 hydrogen bonds · protein-protein
- A–F · 224 Ų buried · 0 hydrogen bonds · protein-nucleic
- B–H · 219 Ų buried · 2 hydrogen bonds · protein-nucleic
Compared structures
- 7DWR · Structure of Sulfolobus solfataricus SegA-ADP complex bound to DNA · the same entry in another collection · chain D against D, 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 Q981B3
- Elsewhere: RCSB PDB 7DWR · PDBe 7DWR · UniProt Q981B3
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