MolNFT v1 · #34969 · protein + DNA
Crystal structure of the pria protein complexed with oligonucleotides
2DWN · Primosomal protein N': “Crystal structure of the pria protein complexed with oligonucleotides”. X-ray diffraction, 6 pockets (best druggability 0.71). MolNFT v1 #34969 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2DWN
- Type
- protein + DNA
- Length
- 419 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Primosomal protein N'; DNA (5'-D(*A*G)-3')
- EC
- 3.6.4.-
- UniProt
- P17888
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 25% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Primosomal protein N' (EC 3.6.4.-) | protein | 105 | 28% helix, 28% strand | P17888 |
| B | Primosomal protein N' (EC 3.6.4.-) | protein | 104 | 24% helix, 20% strand | P17888 |
| D | Primosomal protein N' (EC 3.6.4.-) | protein | 103 | 22% helix, 27% strand | P17888 |
| E, F | DNA (5'-D(*A*G)-3') | dna | 1 | — | — |
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 536 | 0.71 | 0.80 | 43 | empty |
| 2 | 671 | 0.71 | 0.78 | 51 | empty |
| 3 | 77 | 0.46 | 0.82 | 22 | empty |
| 4 | 80 | 0.45 | 0.81 | 20 | empty |
| 5 | 55 | 0.40 | 0.82 | 20 | empty |
Interfaces
8 interfaces between chains.
- C–D · 2179 Ų buried · 42 hydrogen bonds · protein-protein
- A–B · 2079 Ų buried · 38 hydrogen bonds · protein-protein
- A–C · 813 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 250 Ų buried · 3 hydrogen bonds · protein-protein
- A–E · 227 Ų buried · 10 hydrogen bonds · protein-nucleic
Compared structures
- 2DWN · 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 0.83
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 2DWN · PDBe 2DWN · UniProt P17888
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