MolNFT v1 · #182860 · protein
Crystal structure of deoxyuridine 5'-triphosphate nucleotidohydrolase from rickettsia prowazekii str. madrid E in complex with 2'- deoxyuridine 5'-monophoephate (dump)
7N6S: “Crystal structure of deoxyuridine 5'-triphosphate nucleotidohydrolase from rickettsia prowazekii str. madrid…”. X-ray diffraction, 1 ligand (UMP), 16 pockets (best druggability 0.80). MolNFT v1 #182860 on GenesisL1: 3D structure…
- PDB
- 7N6S
- Type
- protein
- Length
- 860 residues
- Chains
- 6
- 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
- UMP
- Pockets
- 16 · best druggability 0.80
Structure
x-ray diffraction · 5 distinct chains · 5% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23) | protein | 135 | 5% helix, 48% strand | Q9ZDD2 |
| B | Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23) | protein | 146 | 5% helix, 47% strand | Q9ZDD2 |
| C, E | Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23) | protein | 147 | 5% helix, 42% strand | Q9ZDD2 |
| D | Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23) | protein | 139 | 5% helix, 47% strand | Q9ZDD2 |
| F | Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23) | protein | 146 | 5% helix, 43% strand | Q9ZDD2 |
Ligands and binding sites
- UMP · 2'-deoxyuridine 5'-monophosphate · ligand · 6 copies · chains A, B, D, C, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 952 | 0.80 | 0.82 | 106 | UMP |
| 2 | 97 | 0.78 | 0.98 | 32 | empty |
| 3 | 81 | 0.75 | 0.98 | 23 | empty |
| 4 | 243 | 0.68 | 0.84 | 38 | UMP |
| 5 | 210 | 0.59 | 0.80 | 25 | UMP |
Interfaces
11 interfaces between chains.
- C–F · 2310 Ų buried · 39 hydrogen bonds · protein-protein
- C–E · 2191 Ų buried · 32 hydrogen bonds · protein-protein
- E–F · 2033 Ų buried · 34 hydrogen bonds · protein-protein
- A–D · 1964 Ų buried · 34 hydrogen bonds · protein-protein
- B–D · 1836 Ų buried · 38 hydrogen bonds · protein-protein
Compared structures
- 7N6S · Crystal Structure of deoxyuridine 5'-triphosphate nucleotidohydrolase from Rickettsia… · the same entry in another collection · chain F against F, TM-score 1.00
- Q9ZDD2 · AlphaFold monomer V2.0 prediction for deoxyuridine 5'-triphosphate nucleotidohydrolase… · a predicted model of the same protein · chain D against A, TM-score 0.97
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 7N6S · PDBe 7N6S · UniProt Q9ZDD2
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