Research workbench
Aquifex aeolicus replicative helicase (dnab) complexed with ADP, at 3.3 resolution
Analyse Aquifex aeolicus replicative helicase (dnab) complexed with ADP, at 3.3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NMN
- Type
- protein
- Length
- 837 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Replicative DNA helicase
- UniProt
- O67450
- Ligands
- ADP, MG, SR
- Pockets
- 9 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Replicative DNA helicase | protein | 425 | 54% helix, 13% strand | O67450 |
| B | Replicative DNA helicase | protein | 412 | 54% helix, 14% strand | O67450 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- SR · Strontium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1162 | 0.84 | 0.85 | 125 | empty |
| 2 | 521 | 0.74 | 0.82 | 55 | ADP |
| 3 | 412 | 0.68 | 0.80 | 39 | empty |
| 4 | 134 | 0.55 | 0.83 | 24 | empty |
| 5 | 90 | 0.51 | 0.82 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 2706 Ų buried · 35 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4NMN · Aquifex aeolicus replicative helicase (DnaB) complexed with ADP, at 3.3 resolution · 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 O67450
- Elsewhere: RCSB PDB 4NMN · PDBe 4NMN · UniProt O67450
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