Research workbench
Mycobacterium tuberculosis dutpase complexed with dutp in the absence of metal ion.
Analyse Mycobacterium tuberculosis dutpase complexed with dutp in the absence of metal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1SMC
- Type
- protein
- Length
- 397 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
- DUT, NO3
- Pockets
- 6 · best druggability 0.56
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 | 130 | 5% helix, 42% strand | P0A552 |
| B | Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23) | protein | 138 | 8% helix, 41% strand | P0A552 |
| C | Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23) | protein | 129 | 5% helix, 47% strand | P0A552 |
Ligands and binding sites
- DUT · Deoxyuridine-5'-triphosphate · ligand · 3 copies · chains A, B, C
- NO3 · Nitrate ion · ion · chains A, C
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 3 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 189 | 0.56 | 0.80 | 31 | DUT |
| 2 | 209 | 0.52 | 0.77 | 28 | DUT |
| 3 | 180 | 0.50 | 0.77 | 21 | TRS |
| 4 | 102 | 0.45 | 0.79 | 18 | DUT |
| 5 | 71 | 0.37 | 0.78 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1706 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 1703 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 1582 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 1SMC · Mycobacterium tuberculosis dUTPase complexed with dUTP in the absence of metal ion. · 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 1SMC · PDBe 1SMC · UniProt P0A552
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