Research workbench
Hybrid structure of the pRN1 helix bundle domain in complex with DNA and 2 ATP molecules
Analyse Hybrid structure of the pRN1 helix bundle domain in complex with DNA and 2 ATP… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GVT
- Type
- protein + DNA
- Length
- 124 residues
- Chains
- 2
- Method
- solution nmr, solid-state nmr
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- NOT
- Source
- Sulfolobus islandicus; SYNTHETIC CONSTRUCT
- 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 · resolution NOT · 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
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