Research workbench
Vaccinia virus protein VP39 in complex with S-adenosylhomocysteine
Analyse Vaccinia virus protein VP39 in complex with S-adenosylhomocysteine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1VP3
- Type
- protein
- Length
- 291 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VP39
- EC
- 2.7.7.19
- UniProt
- P07617
- Ligands
- SAH
- Pockets
- 4 · best druggability 0.51
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VP39 (EC 2.7.7.19) | protein | 291 | 41% helix, 17% strand | P07617 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 184 | 0.51 | 0.77 | 37 | empty |
| 2 | 79 | 0.37 | 0.77 | 21 | empty |
| 3 | 75 | 0.35 | 0.76 | 24 | SAH |
| 4 | 76 | 0.34 | 0.75 | 12 | empty |
Compared structures
- 1VP3 · Vaccinia virus protein VP39 in complex with S-adenosylhomocysteine · 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 P07617
- Elsewhere: RCSB PDB 1VP3 · PDBe 1VP3 · UniProt P07617
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