Research workbench
Crystal structure of dutpase complexed with substrate analogue methylene-dutp
Analyse Crystal structure of dutpase complexed with substrate analogue methylene-dutp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2HRM
- Type
- protein
- Length
- 137 residues
- Chains
- 1
- 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
- UC5
- Pockets
- 1 · best druggability 0.42
Structure
x-ray diffraction · 1 distinct chain · 5% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23) | protein | 137 | 5% helix, 42% strand | P06968 |
Ligands and binding sites
- UC5 · 2'-deoxy-5'-O-[(S)-hydroxy(phosphonomethyl)phosphoryl]uridine · ligand · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 112 | 0.42 | 0.76 | 19 | empty |
Compared structures
- 2HRM · Crystal structure of dUTPase complexed with substrate analogue methylene-dUTP · 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 A against A, TM-score 0.99
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 2HRM · PDBe 2HRM · UniProt P06968
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