Research workbench
Structure of DNA helicase with adpnp
Analyse Structure of DNA helicase with adpnp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1QHH
- Type
- protein
- Length
- 623 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (pcra (subunit))
- UniProt
- P56255
- Ligands
- ATP
- Pockets
- 5 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 54% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein (pcra (subunit)) | protein | 164 | 59% helix, 10% strand | P56255 |
| B | Protein (pcra (subunit)) | protein | 261 | 52% helix, 13% strand | P56255 |
| C | Protein (pcra (subunit)) | protein | 102 | 75% helix, 0% strand | P56255 |
| D | Protein (pcra (subunit)) | protein | 96 | 28% helix, 38% strand | P56255 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 653 | 0.68 | 0.77 | 71 | ATP |
| 2 | 292 | 0.61 | 0.79 | 36 | empty |
| 3 | 257 | 0.56 | 0.77 | 29 | empty |
| 4 | 126 | 0.45 | 0.77 | 29 | empty |
| 5 | 77 | 0.40 | 0.78 | 18 | empty |
Interfaces
6 interfaces between chains.
- A–B · 4338 Ų buried · 53 hydrogen bonds · protein-protein
- B–D · 3799 Ų buried · 71 hydrogen bonds · protein-protein
- B–C · 1802 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 239 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 220 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
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 P56255
- Elsewhere: RCSB PDB 1QHH · PDBe 1QHH · UniProt P56255
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