Research workbench
Mycobacterium tuberculosis dutpase complexed with magnesium and dudp
Analyse Mycobacterium tuberculosis dutpase complexed with magnesium and dudp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1SLH
- Type
- protein
- Length
- 405 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
- DUD, MG
- Pockets
- 5 · best druggability 0.71
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 | 135 | 7% helix, 43% strand | P0A552 |
| B | Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23) | protein | 140 | 4% helix, 42% strand | P0A552 |
| C | Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23) | protein | 130 | 5% helix, 44% strand | P0A552 |
Ligands and binding sites
- DUD · Deoxyuridine-5'-diphosphate · ligand · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
- 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
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 70 | 0.71 | 0.96 | 23 | TRS |
| 2 | 268 | 0.57 | 0.78 | 31 | DUD, MG |
| 3 | 204 | 0.53 | 0.77 | 29 | MG, DUD |
| 4 | 167 | 0.50 | 0.78 | 29 | MG, DUD |
| 5 | 164 | 0.49 | 0.77 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1747 Ų buried · 31 hydrogen bonds · protein-protein
- A–C · 1664 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 1603 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 1SLH · Mycobacterium tuberculosis dUTPase complexed with magnesium and dUDP · 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 1SLH · PDBe 1SLH · UniProt P0A552
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