Research workbench
Protein-DNA complex of vaccinia virus D4 with double-stranded non- specific DNA
Analyse Protein-DNA complex of vaccinia virus D4 with double-stranded non- specific DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4QCB
- Type
- protein + DNA
- Length
- 448 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uracil-DNA glycosylase; 5'-D(*GP*CP*AP*AP*AP*CP*GP*TP*TP*TP*GP*C)-3'
- EC
- 3.2.2.27
- UniProt
- P04303
- Pockets
- 3 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Uracil-DNA glycosylase (EC 3.2.2.27) | protein | 213 | 41% helix, 17% strand | P04303 |
| C | 5'-D(*GP*CP*AP*AP*AP*CP*GP*TP*TP*TP*GP*C)-3' | dna | 12 | — | — |
| D | 5'-D(*GP*CP*AP*AP*AP*CP*GP*TP*TP*TP*GP*C)-3' | dna | 10 | — | — |
Ligands and binding sites
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 968 | 0.74 | 0.77 | 79 | GOL |
| 2 | 381 | 0.68 | 0.81 | 45 | GOL |
| 3 | 408 | 0.66 | 0.80 | 46 | GOL |
Interfaces
6 interfaces between chains.
- C–D · 483 Ų buried · 59 hydrogen bonds · nucleic-nucleic
- A–B · 328 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 308 Ų buried · 7 hydrogen bonds · protein-nucleic
- A–D · 305 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–C · 117 Ų buried · 1 hydrogen bond · protein-nucleic
Compared structures
- 4QCB · Protein-DNA complex of Vaccinia virus D4 with double-stranded non-specific 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 P04303
- Elsewhere: RCSB PDB 4QCB · PDBe 4QCB · UniProt P04303
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