Research workbench
Structure of SCPIF1 in complex with tttgggtt and ADP-ALF4
Analyse Structure of SCPIF1 in complex with tttgggtt and ADP-ALF4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5O6E
- Type
- protein + DNA
- Length
- 1,037 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent DNA helicase PIF1; DNA (5'-D(*TP*TP*TP*GP*GP*T)-3')
- EC
- 3.6.4.12
- UniProt
- P07271
- Ligands
- ADP, ALF, MG, CL
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-dependent DNA helicase PIF1 (EC 3.6.4.12) | protein | 512 | 37% helix, 18% strand | P07271 |
| B | ATP-dependent DNA helicase PIF1 (EC 3.6.4.12) | protein | 513 | 35% helix, 19% strand | P07271 |
| C, D | DNA (5'-D(*TP*TP*TP*GP*GP*T)-3') | dna | 6 | — | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- ALF · Tetrafluoroaluminate ion · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 452 | 0.81 | 0.89 | 54 | empty |
| 2 | 253 | 0.74 | 0.88 | 30 | empty |
| 3 | 291 | 0.71 | 0.85 | 34 | empty |
| 4 | 119 | 0.68 | 0.91 | 22 | empty |
| 5 | 654 | 0.68 | 0.77 | 79 | ADP, ALF, MG |
Interfaces
6 interfaces between chains.
- A–B · 1080 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 1060 Ų buried · 12 hydrogen bonds · protein-nucleic
- B–D · 973 Ų buried · 7 hydrogen bonds · protein-nucleic
- A–D · 142 Ų buried · 3 hydrogen bonds · protein-nucleic
- B–C · 73 Ų buried · 2 hydrogen bonds · protein-nucleic
Compared structures
- 5O6E · Structure of ScPif1 in complex with TTTGGGTT and ADP-AlF4 · the same entry in another collection · chain A against A, TM-score 1.00
- P07271 · AlphaFold monomer V2.0 prediction for ATP-dependent DNA helicase PIF1 (P07271) · a predicted model of the same protein · chain B against A, TM-score 0.70
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 P07271
- Elsewhere: RCSB PDB 5O6E · PDBe 5O6E · UniProt P07271
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