Research workbench
Crystal structures of feline immunodeficiency virus dutp pyrophosphatase and its nucleotide complexes in three crystal forms.
Analyse Crystal structures of feline immunodeficiency virus dutp pyrophosphatase and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1F7P
- Type
- protein
- Length
- 347 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pol polyprotein
- EC
- 3.6.1.23
- UniProt
- P16088
- Ligands
- UDP
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 3% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Pol polyprotein (EC 3.6.1.23) | protein | 116 | 3% helix, 49% strand | P16088 |
| C | Pol polyprotein (EC 3.6.1.23) | protein | 115 | 3% helix, 49% strand | P16088 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 2 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 225 | 0.82 | 0.95 | 32 | empty |
| 2 | 102 | 0.47 | 0.80 | 19 | empty |
| 3 | 119 | 0.43 | 0.77 | 22 | UDP |
| 4 | 103 | 0.37 | 0.75 | 25 | UDP |
| 5 | 66 | 0.33 | 0.76 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1452 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 1410 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1285 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 1F7P · Crystal structures of feline immunodeficiency virus dutp pyrophosphatase and its… · 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 P16088
- Elsewhere: RCSB PDB 1F7P · PDBe 1F7P · UniProt P16088
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