Research workbench
Native crystal structure analysis on arabidopsis dutpase
Analyse Native crystal structure analysis on arabidopsis dutpase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PC5
- Type
- protein
- Length
- 380 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dutp pyrophosphatase-like protein
- EC
- 3.6.1.23
- UniProt
- Q9STG6
- Ligands
- MG
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Dutp pyrophosphatase-like protein (EC 3.6.1.23) | protein | 127 | 6% helix, 46% strand | Q9STG6 |
| B | Dutp pyrophosphatase-like protein (EC 3.6.1.23) | protein | 126 | 6% helix, 44% strand | Q9STG6 |
Ligands and binding sites
- MG · Magnesium ion · metal · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 115 | 0.79 | 0.98 | 26 | empty |
| 2 | 151 | 0.47 | 0.77 | 29 | empty |
| 3 | 178 | 0.47 | 0.76 | 29 | empty |
| 4 | 123 | 0.41 | 0.75 | 26 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1645 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 1599 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 1543 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 2PC5 · Native crystal structure analysis on Arabidopsis dUTPase · the same entry in another collection · chain A against A, TM-score 1.00
- Q9STG6 · AlphaFold monomer V2.0 prediction for deoxyuridine 5'-triphosphate nucleotidohydrolase… · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q9STG6
- Elsewhere: RCSB PDB 2PC5 · PDBe 2PC5 · UniProt Q9STG6
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