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2.7 ångström resolution crystal structure of a probable holliday junction DNA helicase (ruvb) from campylobacter jejuni subsp. jejuni nctc 11168 in complex with adenosine-5'-diphosphate
Analyse 2.7 ångström resolution crystal structure of a probable holliday junction DNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PFI
- Type
- protein
- Length
- 584 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Holliday junction ATP-dependent DNA helicase ruvb
- EC
- 3.6.4.12
- UniProt
- A3ZGU7
- Ligands
- ADP
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Holliday junction ATP-dependent DNA helicase ruvb (EC 3.6.4.12) | protein | 301 | 52% helix, 12% strand | A3ZGU7 |
| B | Holliday junction ATP-dependent DNA helicase ruvb (EC 3.6.4.12) | protein | 283 | 53% helix, 13% strand | A3ZGU7 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 931 | 0.80 | 0.82 | 108 | ADP |
| 2 | 277 | 0.63 | 0.81 | 33 | ADP |
| 3 | 125 | 0.38 | 0.74 | 22 | empty |
| 4 | 59 | 0.31 | 0.75 | 12 | empty |
| 5 | 54 | 0.27 | 0.74 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 1373 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 3PFI · 2.7 Angstrom resolution crystal structure of a probable holliday junction DNA helicase… · 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 A3ZGU7
- Elsewhere: RCSB PDB 3PFI · PDBe 3PFI · UniProt A3ZGU7
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