MolNFT v1 · #25379 · protein
AS11 variant of vaccinia virus protein VP39 in complex with S- adenosyl-L-methionine
1VPT: “AS11 variant of vaccinia virus protein VP39 in complex with S- adenosyl-L-methionine”. X-ray diffraction, 1 ligand (SAM), 4 pockets (best druggability 0.53). MolNFT v1 #25379 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1VPT
- 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
- SAM
- Pockets
- 4 · best druggability 0.53
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
- SAM · S-adenosylmethionine · 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 | 172 | 0.53 | 0.79 | 38 | empty |
| 2 | 97 | 0.39 | 0.77 | 19 | empty |
| 3 | 94 | 0.37 | 0.75 | 25 | SAM |
| 4 | 70 | 0.33 | 0.75 | 13 | empty |
Compared structures
- 1VPT · AS11 variant of vaccinia virus protein VP39 in complex with S-adenosyl-L-methionine · 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 1VPT · PDBe 1VPT · UniProt P07617
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