Research workbench
Crystal structure of C-terminal domain of helicobacter pylori dnab helicase
Analyse Crystal structure of C-terminal domain of helicobacter pylori dnab helicase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4A1F
- Type
- protein
- Length
- 630 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Replicative DNA helicase
- EC
- 3.6.4.12
- UniProt
- O25916
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Replicative DNA helicase (EC 3.6.4.12) | protein | 323 | 50% helix, 20% strand | O25916 |
| B | Replicative DNA helicase (EC 3.6.4.12) | protein | 307 | 49% helix, 21% strand | O25916 |
Ligands and binding sites
- FLC · Citrate anion · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 574 | 0.78 | 0.84 | 52 | empty |
| 2 | 575 | 0.78 | 0.84 | 65 | empty |
| 3 | 104 | 0.57 | 0.85 | 17 | empty |
| 4 | 208 | 0.51 | 0.77 | 26 | empty |
| 5 | 141 | 0.49 | 0.79 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 1931 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (additive adduct).
Compared structures
- 4A1F · Crystal structure of C-terminal domain of Helicobacter pylori DnaB Helicase · the same entry in another collection · chain A against A, 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 0.88
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 4A1F · PDBe 4A1F · UniProt O25916
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