MolNFT v1 · #123469 · protein
Vaccinia virus D4/A20(1-50)W43A mutant
5JKR · Uracil-DNA glycosylase: “Vaccinia virus D4/A20(1-50)W43A mutant”. X-ray diffraction, 1 ligand (SO4), 3 pockets (best druggability 0.71). MolNFT v1 #123469 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5JKR
- Type
- protein
- Length
- 542 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 0.71
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 15% 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 | 67% helix, 0% strand | P20995 |
| A | Uracil-DNA glycosylase (EC 3.2.2.27) | protein | 219 | 37% helix, 17% strand | P20536 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 796 | 0.71 | 0.77 | 79 | empty |
| 2 | 95 | 0.53 | 0.84 | 18 | empty |
| 3 | 83 | 0.51 | 0.83 | 20 | SO4 |
Interfaces
3 interfaces between chains.
- A–C · 883 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 874 Ų buried · 9 hydrogen bonds · protein-protein
- B–A · 508 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5JKR · vaccinia virus D4/A20(1-50)w43a mutant · 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 5JKR · PDBe 5JKR · UniProt P20536 · UniProt P20995
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