Research workbench
Three-dimensional structure of N-terminal domain of dnab helicase from helicobacter pylori and its interactions with primase
Analyse Three-dimensional structure of N-terminal domain of dnab helicase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GXV
- Type
- protein
- Length
- 293 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Replicative DNA helicase
- EC
- 3.6.1.-
- UniProt
- O25916
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 72% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Replicative DNA helicase (EC 3.6.1.-) | protein | 122 | 71% helix, 0% strand | O25916 |
| B | Replicative DNA helicase (EC 3.6.1.-) | protein | 123 | 69% helix, 0% strand | O25916 |
| C | Replicative DNA helicase (EC 3.6.1.-) | protein | 22 | 82% helix, 0% strand | O25916 |
| D | Replicative DNA helicase (EC 3.6.1.-) | protein | 26 | 81% helix, 0% strand | O25916 |
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 682 | 0.72 | 0.79 | 51 | empty |
| 2 | 69 | 0.37 | 0.78 | 17 | empty |
| 3 | 52 | 0.30 | 0.76 | 13 | empty |
| 4 | 64 | 0.30 | 0.74 | 13 | empty |
Interfaces
5 interfaces between chains.
- A–B · 597 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 392 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 376 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 143 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 96 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3GXV · Three-dimensional structure of N-terminal domain of DnaB Helicase from Helicobacter… · the same entry in another collection · chain D against D, TM-score 1.00
- O25916 · AlphaFold monomer V2.0 prediction for replicative DNA helicase (O25916) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 O25916
- Elsewhere: RCSB PDB 3GXV · PDBe 3GXV · UniProt O25916
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