Research workbench
Structure of escherichia COLI dutpase Q93H mutant
Analyse Structure of escherichia COLI dutpase Q93H mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HDE
- Type
- protein
- Length
- 437 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
- P06968
- Ligands
- DUP, MG
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23) | protein | 148 | 5% helix, 46% strand | P06968 |
| B | Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23) | protein | 152 | 5% helix, 45% strand | P06968 |
| C | Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23) | protein | 137 | 5% helix, 51% strand | P06968 |
Ligands and binding sites
- DUP · 2'-deoxyuridine 5'-alpha,beta-imido-triphosphate · ligand · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 147 | 0.77 | 0.95 | 31 | DUP, MG |
| 2 | 141 | 0.77 | 0.95 | 31 | DUP, MG |
| 3 | 214 | 0.51 | 0.76 | 35 | DUP, MG |
| 4 | 74 | 0.29 | 0.73 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2467 Ų buried · 39 hydrogen bonds · protein-protein
- B–C · 2239 Ų buried · 47 hydrogen bonds · protein-protein
- A–C · 1953 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 6HDE · Structure of Escherichia coli dUTPase Q93H mutant · the same entry in another collection · chain A against A, TM-score 1.00
- P06968 · AlphaFold monomer V2.0 prediction for deoxyuridine 5'-triphosphate nucleotidohydrolase… · a predicted model of the same protein · chain B 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 P06968
- Elsewhere: RCSB PDB 6HDE · PDBe 6HDE · UniProt P06968
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