MolNFT v1 · #174975 · protein + DNA
Sulfur binding domain of sprmcra complexed with phosphorothioated DNA
7CCD · Hnhc domain-containing protein: “Sulfur binding domain of sprmcra complexed with phosphorothioated DNA”. X-ray diffraction, 4 pockets (best druggability 0.79). MolNFT v1 #174975 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 7CCD
- Type
- protein + DNA
- Length
- 373 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hnhc domain-containing protein; DNA (5'-D(*CP*AP*CP*GP*TP*TP*CP*GP*CP*C)-3'); DNA…
- UniProt
- A0A0M4DML1
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 57% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hnhc domain-containing protein | protein | 169 | 56% helix, 8% strand | A0A0M4DML1 |
| E, C | DNA (5'-D(*CP*AP*CP*GP*TP*TP*CP*GP*CP*C)-3') | dna | 10 | — | — |
| F, D | DNA (5'-D(*GP*GP*CP*GP*AS*AP*CP*GP*TP*G)-3') | dna | 10 | — | — |
| B | Hnhc domain-containing protein | protein | 164 | 58% helix, 8% strand | A0A0M4DML1 |
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 473 | 0.79 | 0.87 | 40 | empty |
| 2 | 50 | 0.29 | 0.75 | 13 | empty |
| 3 | 56 | 0.28 | 0.75 | 15 | empty |
| 4 | 61 | 0.28 | 0.74 | 15 | empty |
Interfaces
12 interfaces between chains.
- B–D · 626 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–F · 618 Ų buried · 15 hydrogen bonds · protein-nucleic
- E–F · 479 Ų buried · 55 hydrogen bonds · nucleic-nucleic
- C–D · 468 Ų buried · 47 hydrogen bonds · nucleic-nucleic
- B–C · 322 Ų buried · 2 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 7CCD · 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 7CCD · PDBe 7CCD · UniProt A0A0M4DML1
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