Research workbench
Vaccinia virus D4 P173G mutant /A20(1-50)
Analyse Vaccinia virus D4 P173G mutant /A20(1-50) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JKT
- Type
- protein
- Length
- 543 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uracil-DNA glycosylase; DNA polymerase processivity factor component A20
- EC
- 3.2.2.27
- UniProt
- P20536, P20995
- Ligands
- SO4
- Pockets
- 3 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Uracil-DNA glycosylase (EC 3.2.2.27) | protein | 221 | 38% helix, 17% strand | P20536 |
| D, C | DNA polymerase processivity factor component A20 | protein | 51 | 63% helix, 0% strand | P20995 |
| A | Uracil-DNA glycosylase (EC 3.2.2.27) | protein | 220 | 37% helix, 18% strand | P20536 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 5 copies · chains B, A
- ACT · Acetate ion · additive · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 797 | 0.70 | 0.77 | 85 | empty |
| 2 | 87 | 0.50 | 0.83 | 19 | SO4, ACT |
| 3 | 86 | 0.49 | 0.82 | 18 | ACT |
Interfaces
3 interfaces between chains.
- B–D · 978 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 954 Ų buried · 9 hydrogen bonds · protein-protein
- B–A · 551 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5JKT · vaccinia virus D4 P173G mutant /A20(1-50) · the same entry in another collection · chain B against B, 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 5JKT · PDBe 5JKT · UniProt P20536 · UniProt P20995
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.