MolNFT v1 · #150512 · protein + DNA
Hybrid structure of the PRN1 helix bundle domain in complex with DNA and 2 ATP molecules
6GVT · DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3'): “Hybrid structure of the PRN1 helix bundle domain in complex with DNA and 2 ATP molecules”. Solution nmr; solid-state nmr, 2 ligands (ATP, MG), 1 pocket (best druggability 0.39). MolNFT v1…
- PDB
- 6GVT
- Type
- protein + DNA
- Length
- 124 residues
- Chains
- 2
- Method
- solution nmr; solid-state nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3'); Functional PRN1 primase
- UniProt
- Q54324
- Ligands
- ATP, MG
- Pockets
- 1 · best druggability 0.39
Structure
solution nmr; solid-state nmr · 2 distinct chains · 63% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3') | dna | 9 | — | — |
| B | Functional PRN1 primase | protein | 115 | 63% helix, 0% strand | Q54324 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 92 | 0.39 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 682 Ų buried · 15 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6GVT · Hybrid structure of the pRN1 helix bundle domain in complex with DNA and 2 ATP molecules · 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 Q54324
- Elsewhere: RCSB PDB 6GVT · PDBe 6GVT · UniProt Q54324
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.