Research workbench
Structure of YNCF,THE genomic dutpase from bacillus subtilis
Analyse Structure of YNCF,THE genomic dutpase from bacillus subtilis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XCD
- Type
- protein
- Length
- 774 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable deoxyuridine 5'-triphosphate nucleotidohydrolase yncf
- EC
- 3.6.1.23
- UniProt
- O31801
- Ligands
- NA, MG, CL
- Pockets
- 8 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 4% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Probable deoxyuridine 5'-triphosphate nucleotidohydrolase yncf (EC 3.6.1.23) | protein | 129 | 4% helix, 50% strand | O31801 |
Ligands and binding sites
- NA · Sodium ion · metal · 6 copies · chains A, B, F, C, D, E
- MG · Magnesium ion · metal · 2 copies · chains A, B, C, D, E, F
- CL · Chloride ion · ion · 3 copies · chains C, F
- GOL · Glycerol · additive · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 838 | 0.76 | 0.80 | 73 | NA, GOL |
| 2 | 816 | 0.72 | 0.78 | 67 | CL, NA |
| 3 | 248 | 0.55 | 0.77 | 50 | NA |
| 4 | 272 | 0.55 | 0.76 | 40 | empty |
| 5 | 211 | 0.54 | 0.78 | 30 | empty |
Interfaces
8 interfaces between chains.
- E–F · 1521 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 1515 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1505 Ų buried · 21 hydrogen bonds · protein-protein
- D–F · 1502 Ų buried · 23 hydrogen bonds · protein-protein
- D–E · 1481 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 2XCD · Structure of YncF,the genomic dUTPase from Bacillus subtilis · the same entry in another collection · chain C against C, TM-score 1.00
- O31801 · AlphaFold monomer V2.0 prediction for probable deoxyuridine 5'-triphosphate… · a predicted model of the same protein · chain A against A, TM-score 0.96
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 O31801
- Elsewhere: RCSB PDB 2XCD · PDBe 2XCD · UniProt O31801
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