MolNFT v1 · #179872 · protein + DNA
Muscovy duck circovirus rep domain complexed with a single-stranded DNA 10-mer comprising the cleavage site
7KIJ · ATP-dependent helicase rep: “Muscovy duck circovirus rep domain complexed with a single-stranded DNA 10-mer comprising the cleavage site”. X-ray diffraction, 2 ligands (MN, SO4), 1 pocket (best druggability 0.29). MolNFT v1 #179872…
- PDB
- 7KIJ
- Type
- protein + DNA
- Length
- 217 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent helicase rep; DNA (5'-D(*TP*AP*TP*TP*AP*TP*TP*AP*CP*C)-3')
- UniProt
- D2JZX8
- Ligands
- MN, SO4
- Pockets
- 1 · best druggability 0.29
Structure
x-ray diffraction · 4 distinct chains · 25% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | ATP-dependent helicase rep | protein | 100 | 25% helix, 42% strand | D2JZX8 |
| D | DNA (5'-D(*TP*AP*TP*TP*AP*TP*TP*AP*CP*C)-3') | dna | 9 | — | — |
| A | ATP-dependent helicase rep | protein | 98 | 26% helix, 43% strand | D2JZX8 |
| B | DNA (5'-D(*TP*AP*TP*TP*AP*TP*TP*AP*CP*C)-3') | dna | 10 | — | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains C, B, A
- GOL · Glycerol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 72 | 0.29 | 0.73 | 13 | SO4 |
Interfaces
6 interfaces between chains.
- A–B · 939 Ų buried · 28 hydrogen bonds · protein-nucleic
- C–D · 815 Ų buried · 20 hydrogen bonds · protein-nucleic
- C–B · 312 Ų buried · 7 hydrogen bonds · protein-nucleic
- D–A · 257 Ų buried · 9 hydrogen bonds · protein-nucleic
- C–A · 231 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7KIJ · Muscovy duck circovirus Rep domain complexed with a single-stranded DNA 10-mer comprising… · the same entry in another collection · chain C against C, 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 D2JZX8
- Elsewhere: RCSB PDB 7KIJ · PDBe 7KIJ · UniProt D2JZX8
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