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Crystal structure of deoxyuridine 5'-triphosphate nucleotidohydrolase from rickettsia prowazekii str. madrid E
Analyse Crystal structure of deoxyuridine 5'-triphosphate nucleotidohydrolase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7N56
- Type
- protein
- Length
- 1,606 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxyuridine 5'-triphosphate nucleotidohydrolase
- EC
- 3.6.1.23
- UniProt
- Q9ZDD2
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 7 distinct chains · 5% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E, F, G | Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23) | protein | 132 | 5% helix, 48% strand | Q9ZDD2 |
| C | Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23) | protein | 135 | 5% helix, 48% strand | Q9ZDD2 |
| H | Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23) | protein | 133 | 5% helix, 48% strand | Q9ZDD2 |
| I | Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23) | protein | 136 | 5% helix, 47% strand | Q9ZDD2 |
| J | Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23) | protein | 134 | 5% helix, 47% strand | Q9ZDD2 |
| K | Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23) | protein | 137 | 5% helix, 48% strand | Q9ZDD2 |
| L | Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23) | protein | 139 | 5% helix, 46% strand | Q9ZDD2 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains B, D, J, A, C, I, F, H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 88 | 0.76 | 0.98 | 24 | SO4 |
| 2 | 92 | 0.76 | 0.97 | 27 | SO4 |
| 3 | 84 | 0.75 | 0.98 | 22 | SO4 |
| 4 | 83 | 0.75 | 0.98 | 20 | empty |
| 5 | 399 | 0.60 | 0.76 | 29 | empty |
Interfaces
23 interfaces between chains.
- D–J · 1657 Ų buried · 28 hydrogen bonds · protein-protein
- F–L · 1651 Ų buried · 35 hydrogen bonds · protein-protein
- A–I · 1650 Ų buried · 27 hydrogen bonds · protein-protein
- H–L · 1648 Ų buried · 25 hydrogen bonds · protein-protein
- B–D · 1628 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 7N56 · Crystal Structure of deoxyuridine 5'-triphosphate nucleotidohydrolase from Rickettsia… · the same entry in another collection · chain L against L, 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 Q9ZDD2
- Elsewhere: RCSB PDB 7N56 · PDBe 7N56 · UniProt Q9ZDD2
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