MolNFT v1 · #34967 · protein + DNA
Crystal structure of the pria protein complexed with oligonucleotides
2DWL · 5'-D(*AP*(DC))-3': “Crystal structure of the pria protein complexed with oligonucleotides”. X-ray diffraction, 7 pockets (best druggability 0.75). MolNFT v1 #34967 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2DWL
- Type
- protein + DNA
- Length
- 421 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*AP*(DC))-3'; Primosomal protein N
- EC
- 3.6.1.-
- UniProt
- P17888
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 24% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, F | 5'-D(*AP*(DC))-3' | dna | 2 | — | — |
| A, C | Primosomal protein N (EC 3.6.1.-) | protein | 105 | 24% helix, 25% strand | P17888 |
| B | Primosomal protein N (EC 3.6.1.-) | protein | 104 | 24% helix, 25% strand | P17888 |
| D | Primosomal protein N (EC 3.6.1.-) | protein | 103 | 24% helix, 28% strand | P17888 |
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 596 | 0.75 | 0.82 | 51 | empty |
| 2 | 440 | 0.67 | 0.79 | 46 | empty |
| 3 | 52 | 0.46 | 0.85 | 18 | empty |
| 4 | 65 | 0.44 | 0.82 | 18 | empty |
| 5 | 67 | 0.43 | 0.81 | 21 | empty |
Interfaces
8 interfaces between chains.
- C–D · 2166 Ų buried · 40 hydrogen bonds · protein-protein
- A–B · 2115 Ų buried · 33 hydrogen bonds · protein-protein
- A–C · 809 Ų buried · 9 hydrogen bonds · protein-protein
- E–A · 329 Ų buried · 9 hydrogen bonds · protein-nucleic
- F–C · 310 Ų buried · 9 hydrogen bonds · protein-nucleic
Compared structures
- 2DWL · 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 2DWL · PDBe 2DWL · UniProt P17888
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