Research workbench
Crystal structure of PIF1 helicase from bacteroides in complex with ADP-ALF3 and ssdna
Analyse Crystal structure of PIF1 helicase from bacteroides in complex with ADP-ALF3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FTE
- Type
- protein + DNA
- Length
- 435 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tpr domain protein; 5'-D(*TP*TP*TP*TP*TP*TP)-3'
- EC
- 3.6.4.12
- UniProt
- D7K0H3
- Ligands
- ADP, AF3, MG
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tpr domain protein (EC 3.6.4.12) | protein | 429 | 31% helix, 22% strand | D7K0H3 |
| D | 5'-D(*TP*TP*TP*TP*TP*TP)-3' | dna | 6 | — | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- AF3 · Aluminum fluoride · ligand · chains A
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 555 | 0.73 | 0.81 | 48 | empty |
| 2 | 99 | 0.52 | 0.83 | 28 | empty |
| 3 | 121 | 0.44 | 0.78 | 22 | ADP, AF3, MG |
| 4 | 113 | 0.42 | 0.76 | 22 | empty |
| 5 | 135 | 0.40 | 0.74 | 25 | empty |
Interfaces
1 interface between chains.
- A–D · 922 Ų buried · 10 hydrogen bonds · protein-nucleic
Compared structures
- 5FTE · Crystal structure of Pif1 helicase from Bacteroides in complex with ADP-AlF3 and ssDNA · 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 D7K0H3
- Elsewhere: RCSB PDB 5FTE · PDBe 5FTE · UniProt D7K0H3
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