Research workbench
Crystal structure of the pria protein complexed with oligonucleotides
Analyse Crystal structure of the pria protein complexed with oligonucleotides in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2DWM
- Type
- protein + DNA
- Length
- 421 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*AP*T)-3'; Primosomal protein N
- EC
- 3.6.1.-
- UniProt
- P17888
- Pockets
- 8 · best druggability 0.73
Structure
x-ray diffraction · 5 distinct chains · 24% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, G | 5'-D(*AP*T)-3' | dna | 1 | — | — |
| F | 5'-D(*AP*T)-3' | dna | 2 | — | — |
| A, C | Primosomal protein N (EC 3.6.1.-) | protein | 105 | 25% helix, 22% strand | P17888 |
| B | Primosomal protein N (EC 3.6.1.-) | protein | 104 | 25% helix, 21% strand | P17888 |
| D | Primosomal protein N (EC 3.6.1.-) | protein | 103 | 23% helix, 26% strand | P17888 |
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 623 | 0.73 | 0.80 | 53 | empty |
| 2 | 198 | 0.52 | 0.77 | 21 | empty |
| 3 | 96 | 0.46 | 0.80 | 19 | empty |
| 4 | 97 | 0.43 | 0.79 | 20 | empty |
| 5 | 114 | 0.43 | 0.77 | 19 | empty |
Interfaces
11 interfaces between chains.
- C–D · 2137 Ų buried · 39 hydrogen bonds · protein-protein
- A–B · 2088 Ų buried · 33 hydrogen bonds · protein-protein
- A–C · 800 Ų buried · 10 hydrogen bonds · protein-protein
- F–C · 318 Ų buried · 9 hydrogen bonds · protein-nucleic
- E–A · 247 Ų buried · 6 hydrogen bonds · protein-nucleic
Compared structures
- 2DWM · Crystal structure of the PriA protein complexed with oligonucleotides · the same entry in another collection · chain A against A, TM-score 1.00
- P17888 · AlphaFold monomer V2.0 prediction for primosomal protein N' (P17888) · a predicted model of the same protein · chain D against A, TM-score 0.84
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 P17888
- Elsewhere: RCSB PDB 2DWM · PDBe 2DWM · UniProt P17888
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