MolNFT v1 · #146402 · protein + DNA
Pria helicase bound to dsdna of a DNA replication fork
6DGD · Primosomal protein N': “Pria helicase bound to dsdna of a DNA replication fork”. X-ray diffraction, 2 ligands (ZN, SO4), 20 pockets (best druggability 0.86). MolNFT v1 #146402 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6DGD
- Type
- protein + DNA
- Length
- 1,454 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Primosomal protein N'; DNA (5'-D(P*AP*GP*CP*AP*CP*GP*CP*CP*GP*AP*CP*T)-3'); DNA…
- EC
- 3.6.4.-
- UniProt
- A0A1W2ITH4
- Ligands
- ZN, SO4
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 5 distinct chains · 31% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Primosomal protein N' (EC 3.6.4.-) | protein | 704 | 33% helix, 23% strand | A0A1W2ITH4 |
| B | Primosomal protein N' (EC 3.6.4.-) | protein | 701 | 30% helix, 22% strand | A0A1W2ITH4 |
| W | DNA (5'-D(P*AP*GP*CP*AP*CP*GP*CP*CP*GP*AP*CP*T)-3') | dna | 12 | — | — |
| X, Z | DNA (5'-D(P*GP*TP*CP*GP*GP*CP*GP*TP*GP*CP*TP*C)-3') | dna | 12 | — | — |
| Y | DNA (5'-D(P*GP*AP*GP*CP*AP*CP*GP*CP*CP*GP*AP*CP*T)-3') | dna | 13 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 970 | 0.86 | 0.88 | 143 | SO4 |
| 2 | 1167 | 0.81 | 0.82 | 138 | SO4 |
| 3 | 1009 | 0.77 | 0.79 | 91 | empty |
| 4 | 357 | 0.71 | 0.83 | 40 | empty |
| 5 | 338 | 0.65 | 0.80 | 32 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1310 Ų buried · 18 hydrogen bonds · protein-protein
- W–X · 587 Ų buried · 51 hydrogen bonds · nucleic-nucleic
- Y–Z · 562 Ų buried · 57 hydrogen bonds · nucleic-nucleic
- B–Y · 410 Ų buried · 2 hydrogen bonds · protein-nucleic
- B–Z · 364 Ų buried · 9 hydrogen bonds · protein-nucleic
Compared structures
- 6DGD · PriA helicase bound to dsDNA of a DNA replication fork · the same entry in another collection · chain A against A, TM-score 1.00
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 A0A1W2ITH4
- Elsewhere: RCSB PDB 6DGD · PDBe 6DGD · UniProt A0A1W2ITH4
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