Research workbench
Mycobacterium tuberculosis dutpase complexed with magnesium and deoxyuridine 5'-monophosphate
Analyse Mycobacterium tuberculosis dutpase complexed with magnesium and deoxyuridine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1SNF
- Type
- protein
- Length
- 396 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxyuridine 5'-triphosphate nucleotidohydrolase
- EC
- 3.6.1.23
- UniProt
- P0A552
- Ligands
- UMP, MG, NO3
- Pockets
- 6 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23) | protein | 131 | 5% helix, 43% strand | P0A552 |
| B | Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23) | protein | 136 | 8% helix, 42% strand | P0A552 |
| C | Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23) | protein | 129 | 5% helix, 43% strand | P0A552 |
Ligands and binding sites
- UMP · 2'-deoxyuridine 5'-monophosphate · ligand · 3 copies · chains A, C, B
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
- NO3 · Nitrate ion · ion · 3 copies · chains A, C, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 50 | 0.67 | 0.97 | 18 | TRS |
| 2 | 206 | 0.53 | 0.78 | 32 | MG, UMP |
| 3 | 168 | 0.51 | 0.78 | 27 | UMP, MG |
| 4 | 169 | 0.49 | 0.77 | 21 | empty |
| 5 | 161 | 0.48 | 0.77 | 30 | MG, UMP |
Interfaces
3 interfaces between chains.
- A–B · 1581 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 1549 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 1548 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 1SNF · Mycobacterium tuberculosis dutpase complexed with magnesium and deoxyuridine… · the same entry in another collection · chain A against A, 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 P0A552
- Elsewhere: RCSB PDB 1SNF · PDBe 1SNF · UniProt P0A552
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