MolNFT v1 · #140282 · protein
Crystal structure of the wssv dutpase D88N/R158E mutant in complex with dutp
5Y5Q · WSV112: “Crystal structure of the wssv dutpase D88N/R158E mutant in complex with dutp”. X-ray diffraction, 2 ligands (DUT, MG), 5 pockets (best druggability 0.86). MolNFT v1 #140282 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5Y5Q
- Type
- protein
- Length
- 449 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- WSV112
- UniProt
- Q77J78
- Ligands
- DUT, MG
- Pockets
- 5 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | WSV112 | protein | 148 | 5% helix, 44% strand | Q77J78 |
| B | WSV112 | protein | 161 | 4% helix, 41% strand | Q77J78 |
| C | WSV112 | protein | 140 | 5% helix, 45% strand | Q77J78 |
Ligands and binding sites
- DUT · Deoxyuridine-5'-triphosphate · ligand · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · 3 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 | 299 | 0.86 | 0.96 | 45 | empty |
| 2 | 135 | 0.47 | 0.78 | 21 | DUT, MG |
| 3 | 135 | 0.46 | 0.78 | 23 | MG, DUT |
| 4 | 125 | 0.45 | 0.77 | 21 | DUT, MG |
| 5 | 71 | 0.32 | 0.75 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1637 Ų buried · 32 hydrogen bonds · protein-protein
- B–C · 1619 Ų buried · 32 hydrogen bonds · protein-protein
- A–C · 1575 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 5Y5Q · Crystal structure of the WSSV dUTPase D88N/R158E mutant in complex with dUTP · 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 Q77J78
- Elsewhere: RCSB PDB 5Y5Q · PDBe 5Y5Q · UniProt Q77J78
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