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Vaccinia virus D4/A20(1-50) in complex with dsdna containing an abasic site and free uracyl
Analyse Vaccinia virus D4/A20(1-50) in complex with dsdna containing an abasic site and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YIG
- Type
- protein + DNA
- Length
- 867 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uracil-DNA glycosylase; DNA polymerase processivity factor component A20; DNA…
- EC
- 3.2.2.27
- UniProt
- P20536, P20995
- Ligands
- ORP, URA
- Pockets
- 14 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, I | Uracil-DNA glycosylase (EC 3.2.2.27) | protein | 220 | 38% helix, 15% strand | P20536 |
| B, F, J | DNA polymerase processivity factor component A20 | protein | 50 | 70% helix, 0% strand | P20995 |
| C, G, K | DNA (5'-D(*CP*TP*GP*TP*(ORP)P*AP*TP*CP*TP*T)-3') | dna | 9 | — | — |
| D, H, L | DNA (5'-D(*AP*AP*GP*AP*TP*AP*AP*CP*AP*G)-3') | dna | 10 | — | — |
Ligands and binding sites
- ORP · 2-deoxy-5-phosphono-ribose · ligand · 3 copies · chains A, C, E, G, I, K
- URA · Uracil · ligand · 3 copies · chains A, E, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 82 | 0.75 | 0.97 | 31 | ORP, URA |
| 2 | 840 | 0.71 | 0.76 | 76 | empty |
| 3 | 56 | 0.69 | 0.97 | 19 | ORP, URA |
| 4 | 196 | 0.51 | 0.77 | 25 | empty |
| 5 | 169 | 0.50 | 0.78 | 22 | empty |
Interfaces
21 interfaces between chains.
- I–J · 966 Ų buried · 7 hydrogen bonds · protein-protein
- E–F · 950 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 945 Ų buried · 8 hydrogen bonds · protein-protein
- I–K · 624 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–C · 610 Ų buried · 13 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 6 covalent (covalent ligand).
Compared structures
- 4YIG · vaccinia virus D4/A20(1-50) in complex with dsDNA containing an abasic site and free… · 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 P20536
- Every structure of UniProt P20995
- Elsewhere: RCSB PDB 4YIG · PDBe 4YIG · UniProt P20536 · UniProt P20995
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