Research workbench
Porcine circovirus 2 rep domain complexed with a single-stranded DNA 10-mer comprising the cleavage site
Analyse Porcine circovirus 2 rep domain complexed with a single-stranded DNA 10-mer… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WDZ
- Type
- protein + DNA
- Length
- 336 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*TP*AP*GP*TP*AP*TP*TP*AP*CP*C)-3'); ATP-dependent helicase rep
- UniProt
- A0A060L113
- Ligands
- MN
- Pockets
- 2 · best druggability 0.48
Structure
x-ray diffraction · 5 distinct chains · 27% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, I, F | DNA (5'-D(*TP*AP*GP*TP*AP*TP*TP*AP*CP*C)-3') | dna | 10 | — | — |
| D | ATP-dependent helicase rep | protein | 102 | 27% helix, 39% strand | A0A060L113 |
| G | ATP-dependent helicase rep | protein | 99 | 26% helix, 40% strand | A0A060L113 |
| J | DNA (5'-D(*TP*AP*GP*TP*AP*TP*TP*AP*CP*C)-3') | dna | 4 | — | — |
| A | ATP-dependent helicase rep | protein | 101 | 28% helix, 40% strand | A0A060L113 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 3 copies · chains D, F, I, G, C, A
- EDO · 1,2-ethanediol · additive · 2 copies · chains I, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 59 | 0.48 | 0.85 | 15 | empty |
| 2 | 68 | 0.35 | 0.77 | 16 | empty |
Interfaces
9 interfaces between chains.
- C–A · 958 Ų buried · 31 hydrogen bonds · protein-nucleic
- I–G · 953 Ų buried · 26 hydrogen bonds · protein-nucleic
- D–F · 939 Ų buried · 33 hydrogen bonds · protein-nucleic
- D–A · 383 Ų buried · 2 hydrogen bonds · protein-protein
- G–J · 374 Ų buried · 5 hydrogen bonds · protein-nucleic
Compared structures
- 6WDZ · Porcine circovirus 2 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 A0A060L113
- Elsewhere: RCSB PDB 6WDZ · PDBe 6WDZ · UniProt A0A060L113
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