Research workbench
Structure of SCPIF1 in complex with gggtttt and ADP-ALF4
Analyse Structure of SCPIF1 in complex with gggtttt 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
- 5O6B
- Type
- protein + DNA
- Length
- 1,047 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent DNA helicase PIF1; DNA (5'-D(*GP*GP*GP*TP*TP*T)-3')
- EC
- 3.6.4.12
- UniProt
- P07271
- Ligands
- ADP, ALF, MG, PO4
- Pockets
- 12 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-dependent DNA helicase PIF1 (EC 3.6.4.12) | protein | 528 | 41% helix, 18% strand | P07271 |
| B | ATP-dependent DNA helicase PIF1 (EC 3.6.4.12) | protein | 507 | 41% helix, 19% strand | P07271 |
| C, D | DNA (5'-D(*GP*GP*GP*TP*TP*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
- PO4 · Phosphate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1044 | 0.86 | 0.87 | 123 | empty |
| 2 | 108 | 0.72 | 0.93 | 22 | empty |
| 3 | 758 | 0.71 | 0.77 | 84 | ADP, ALF, MG |
| 4 | 711 | 0.69 | 0.77 | 83 | ADP, ALF, MG |
| 5 | 272 | 0.68 | 0.84 | 52 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1517 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 1012 Ų buried · 20 hydrogen bonds · protein-nucleic
- A–C · 971 Ų buried · 14 hydrogen bonds · protein-nucleic
- A–D · 114 Ų buried · 4 hydrogen bonds · protein-nucleic
- B–C · 109 Ų buried · 2 hydrogen bonds · protein-nucleic
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 P07271
- Elsewhere: RCSB PDB 5O6B · PDBe 5O6B · UniProt P07271
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