Research workbench
Sulfur binding domain of sprmcra complexed with phosphorothioated DNA
Analyse Sulfur binding domain of sprmcra complexed with phosphorothioated DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7CC9
- Type
- protein + DNA
- Length
- 536 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hnhc domain-containing protein; DNA (5'-D(*GP*GP*CP*GP*GS*CP*CP*C)-3'); DNA…
- UniProt
- A0A0M4DML1
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.62
Structure
x-ray diffraction · 4 distinct chains · 56% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Hnhc domain-containing protein | protein | 163 | 56% helix, 8% strand | A0A0M4DML1 |
| B | Hnhc domain-containing protein | protein | 162 | 56% helix, 8% strand | A0A0M4DML1 |
| D, F, H | DNA (5'-D(*GP*GP*CP*GP*GS*CP*CP*C)-3') | dna | 8 | — | — |
| E, G, I | DNA (5'-D(*GP*GP*GP*CP*CP*GP*CP*C)-3') | dna | 8 | — | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 12 copies · chains A, B, I, E, F, G, C
- ACT · Acetate ion · additive · 3 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 567 | 0.62 | 0.75 | 64 | SO4 |
| 2 | 182 | 0.57 | 0.81 | 29 | SO4 |
| 3 | 156 | 0.48 | 0.78 | 27 | empty |
| 4 | 176 | 0.41 | 0.73 | 18 | SO4 |
Interfaces
17 interfaces between chains.
- A–D · 639 Ų buried · 19 hydrogen bonds · protein-nucleic
- B–F · 635 Ų buried · 17 hydrogen bonds · protein-nucleic
- C–H · 611 Ų buried · 18 hydrogen bonds · protein-nucleic
- D–E · 391 Ų buried · 39 hydrogen bonds · nucleic-nucleic
- H–I · 386 Ų buried · 40 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 3 modified (nucleotide modification).
Compared structures
- 7CC9 · Sulfur binding domain of SprMcrA complexed with phosphorothioated 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 A0A0M4DML1
- Elsewhere: RCSB PDB 7CC9 · PDBe 7CC9 · UniProt A0A0M4DML1
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