MolNFT v1 · #21816 · protein
Mycobacterium tuberculosis dutpase complexed with dutp in the absence of metal ion.
1SMC · Deoxyuridine 5'-triphosphate nucleotidohydrolase: “Mycobacterium tuberculosis dutpase complexed with dutp in the absence of metal ion.”. X-ray diffraction, 2 ligands (DUT, NO3), 6 pockets (best druggability 0.56). MolNFT v1 #21816…
- 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
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.