Research workbench
Crystal structure of cytomegalovirus UL44 bound to C-terminal peptide from CMV UL54
Analyse Crystal structure of cytomegalovirus UL44 bound to C-terminal peptide from CMV… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YYP
- Type
- protein
- Length
- 269 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase processivity factor; DNA polymerase
- EC
- 2.7.7.7
- UniProt
- P16790, P08546
- Ligands
- SO4
- Pockets
- 3 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 20% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase processivity factor | protein | 249 | 18% helix, 47% strand | P16790 |
| B | DNA polymerase (EC 2.7.7.7) | protein | 20 | 45% helix, 15% strand | P08546 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 141 | 0.56 | 0.82 | 23 | empty |
| 2 | 143 | 0.42 | 0.75 | 30 | EDO |
| 3 | 66 | 0.36 | 0.78 | 13 | SO4 |
Interfaces
1 interface between chains.
- A–B · 1141 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 1YYP · Crystal structure of cytomegalovirus UL44 bound to C-terminal peptide from CMV UL54 · 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 P16790
- Every structure of UniProt P08546
- Elsewhere: RCSB PDB 1YYP · PDBe 1YYP · UniProt P16790 · UniProt P08546
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