Research workbench
Structure of the bacillus subtilis prophage dutpase with dupnhpp
Analyse Structure of the bacillus subtilis prophage dutpase with dupnhpp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XY3
- Type
- protein
- Length
- 767 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SPBC2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase yoss
- EC
- 3.6.1.23
- UniProt
- O34919
- Ligands
- DUP, MG
- Pockets
- 8 · best druggability 0.72
Structure
x-ray diffraction · 6 distinct chains · 4% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SPBC2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase yoss (EC 3.6.1.23) | protein | 128 | 4% helix, 48% strand | O34919 |
| B | SPBC2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase yoss (EC 3.6.1.23) | protein | 127 | 4% helix, 50% strand | O34919 |
| C | SPBC2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase yoss (EC 3.6.1.23) | protein | 128 | 4% helix, 45% strand | O34919 |
| D | SPBC2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase yoss (EC 3.6.1.23) | protein | 129 | 4% helix, 48% strand | O34919 |
| E | SPBC2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase yoss (EC 3.6.1.23) | protein | 128 | 4% helix, 48% strand | O34919 |
| F | SPBC2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase yoss (EC 3.6.1.23) | protein | 127 | 4% helix, 46% strand | O34919 |
Ligands and binding sites
- DUP · 2'-deoxyuridine 5'-alpha,beta-imido-triphosphate · ligand · 6 copies · chains A, C, B, F, D, E
- MG · Magnesium ion · metal · 3 copies · chains B, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 545 | 0.72 | 0.81 | 50 | DUP, MG |
| 2 | 497 | 0.69 | 0.80 | 51 | DUP |
| 3 | 226 | 0.53 | 0.77 | 29 | DUP |
| 4 | 234 | 0.52 | 0.76 | 29 | DUP |
| 5 | 149 | 0.49 | 0.78 | 22 | DUP, MG |
Interfaces
8 interfaces between chains.
- B–C · 1520 Ų buried · 18 hydrogen bonds · protein-protein
- D–E · 1516 Ų buried · 18 hydrogen bonds · protein-protein
- E–F · 1507 Ų buried · 18 hydrogen bonds · protein-protein
- D–F · 1459 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 1433 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 2XY3 · Structure of the Bacillus subtilis prophage dUTPase with dUpNHpp · the same entry in another collection · chain F against F, TM-score 1.00
- O34919 · AlphaFold monomer V2.0 prediction for spbeta prophage-derived deoxyuridine… · a predicted model of the same protein · chain F 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 O34919
- Elsewhere: RCSB PDB 2XY3 · PDBe 2XY3 · UniProt O34919
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