Research workbench
Bacillus subtilis prophage dutpase in complex with dudp
Analyse Bacillus subtilis prophage dutpase in complex with dudp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Y1T
- Type
- protein
- Length
- 763 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
- DUD
- Pockets
- 9 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 4% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | SPBC2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase yoss (EC 3.6.1.23) | protein | 128 | 4% helix, 49% strand | O34919 |
| C | SPBC2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase yoss (EC 3.6.1.23) | protein | 125 | 4% helix, 50% strand | O34919 |
| E | SPBC2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase yoss (EC 3.6.1.23) | protein | 127 | 4% helix, 49% 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
- DUD · Deoxyuridine-5'-diphosphate · ligand · 5 copies · chains A, B, C, F, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 723 | 0.74 | 0.80 | 62 | DUD |
| 2 | 657 | 0.70 | 0.78 | 52 | DUD |
| 3 | 235 | 0.56 | 0.78 | 33 | DUD |
| 4 | 215 | 0.53 | 0.77 | 30 | empty |
| 5 | 231 | 0.52 | 0.76 | 37 | DUD |
Interfaces
8 interfaces between chains.
- B–C · 1512 Ų buried · 18 hydrogen bonds · protein-protein
- E–F · 1502 Ų buried · 21 hydrogen bonds · protein-protein
- D–E · 1481 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1467 Ų buried · 19 hydrogen bonds · protein-protein
- D–F · 1454 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
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 2Y1T · PDBe 2Y1T · UniProt O34919
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