MolNFT v1 · #174981 · protein + DNA
Sulfur binding domain of sprmcra complexed with phosphorothioated DNA
7CCJ · Hnhc domain-containing protein: “Sulfur binding domain of sprmcra complexed with phosphorothioated DNA”. X-ray diffraction, 3 pockets (best druggability 0.61). MolNFT v1 #174981 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 7CCJ
- Type
- protein + DNA
- Length
- 352 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hnhc domain-containing protein; DNA (5'-D(*GP*GP*AP*TP*CP*AP*TP*C)-3')
- UniProt
- A0A0M4DML1
- Pockets
- 3 · best druggability 0.61
Structure
x-ray diffraction · 4 distinct chains · 56% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hnhc domain-containing protein | protein | 159 | 57% helix, 8% strand | A0A0M4DML1 |
| E, C | DNA (5'-D(*GP*GP*AP*TP*CP*AP*TP*C)-3') | dna | 8 | — | — |
| F, D | DNA (5'-D(*GP*GP*AP*TP*CP*AP*TP*C)-3') | dna | 8 | — | — |
| B | Hnhc domain-containing protein | protein | 161 | 55% helix, 7% strand | A0A0M4DML1 |
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 449 | 0.61 | 0.76 | 33 | empty |
| 2 | 54 | 0.33 | 0.77 | 13 | empty |
| 3 | 52 | 0.30 | 0.76 | 13 | empty |
Interfaces
11 interfaces between chains.
- B–D · 662 Ų buried · 17 hydrogen bonds · protein-nucleic
- A–F · 640 Ų buried · 13 hydrogen bonds · protein-nucleic
- C–D · 345 Ų buried · 19 hydrogen bonds · nucleic-nucleic
- E–F · 345 Ų buried · 21 hydrogen bonds · nucleic-nucleic
- B–C · 273 Ų buried · 2 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 7CCJ · 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 7CCJ · PDBe 7CCJ · UniProt A0A0M4DML1
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