Research workbench
Crystal structure of a PPR1-DNA complex: DNA recognition by proteins containing a ZN2CYS6 binuclear cluster
Analyse Crystal structure of a PPR1-DNA complex: DNA recognition by proteins containing… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1PYI
- Type
- protein + DNA
- Length
- 186 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(*TP*CP*GP*GP*CP*AP*AP*TP*TP*GP*CP*CP*GP*A)-3'); Protein (pyrimidine pathway…
- UniProt
- P07272
- Ligands
- ZN
- Pockets
- 2 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, E | DNA (5'- D(*TP*CP*GP*GP*CP*AP*AP*TP*TP*GP*CP*CP*GP*A)-3') | dna | 14 | — | — |
| A | Protein (pyrimidine pathway regulator 1) | protein | 88 | 35% helix, 7% strand | P07272 |
| B | Protein (pyrimidine pathway regulator 1) | protein | 70 | 43% helix, 6% strand | P07272 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 352 | 0.70 | 0.83 | 32 | empty |
| 2 | 161 | 0.52 | 0.80 | 18 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1729 Ų buried · 9 hydrogen bonds · protein-protein
- D–E · 640 Ų buried · 63 hydrogen bonds · nucleic-nucleic
- D–B · 337 Ų buried · 6 hydrogen bonds · protein-nucleic
- E–A · 333 Ų buried · 4 hydrogen bonds · protein-nucleic
- D–A · 200 Ų buried · 3 hydrogen bonds · protein-nucleic
Compared structures
- 1PYI · Crystal structure of a PPR1-DNA complex: DNA recognition by proteins containing a ZN2CYS6… · the same entry in another collection · chain D against D, TM-score 1.00
- P07272 · AlphaFold monomer V2.0 prediction for pyrimidine pathway regulatory protein 1 (P07272) · a predicted model of the same protein · chain B against A, TM-score 0.86
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 P07272
- Elsewhere: RCSB PDB 1PYI · PDBe 1PYI · UniProt P07272
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