Research workbench
Crystal structure of asfv dutpase
Analyse Crystal structure of asfv dutpase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KZ6
- Type
- protein
- Length
- 433 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E165R
- UniProt
- A0A2X0SE53
- Ligands
- UMP, MG
- Pockets
- 7 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | E165R | protein | 145 | 7% helix, 48% strand | A0A2X0SE53 |
| A | E165R | protein | 141 | 6% helix, 45% strand | A0A2X0SE53 |
| B | E165R | protein | 147 | 6% helix, 44% strand | A0A2X0SE53 |
Ligands and binding sites
- UMP · 2'-deoxyuridine 5'-monophosphate · ligand · 3 copies · chains C, B, A
- MG · Magnesium ion · metal · 2 copies · chains C, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 666 | 0.68 | 0.77 | 75 | UMP |
| 2 | 259 | 0.56 | 0.77 | 37 | MG, UMP |
| 3 | 118 | 0.41 | 0.76 | 22 | UMP, MG |
| 4 | 105 | 0.40 | 0.76 | 19 | empty |
| 5 | 95 | 0.37 | 0.75 | 21 | empty |
Interfaces
3 interfaces between chains.
- C–B · 846 Ų buried · 6 hydrogen bonds · protein-protein
- C–A · 843 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 697 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6KZ6 · Crystal structure of ASFV dUTPase · the same entry in another collection · chain C against C, 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 A0A2X0SE53
- Elsewhere: RCSB PDB 6KZ6 · PDBe 6KZ6 · UniProt A0A2X0SE53
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