Research workbench
Structure of SCPIF1 in complex with polydt and atpgs
Analyse Structure of SCPIF1 in complex with polydt and atpgs in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5O6D
- Type
- protein + DNA
- Length
- 1,066 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent DNA helicase PIF1; DNA (5'-D(P*TP*TP*TP*TP*TP*T)-3')
- EC
- 3.6.4.12
- UniProt
- P07271
- Ligands
- AGS, MG
- Pockets
- 16 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | ATP-dependent DNA helicase PIF1 (EC 3.6.4.12) | protein | 527 | 37% helix, 15% strand | P07271 |
| C, D | DNA (5'-D(P*TP*TP*TP*TP*TP*T)-3') | dna | 6 | — | — |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 822 | 0.78 | 0.81 | 57 | empty |
| 2 | 547 | 0.71 | 0.80 | 54 | empty |
| 3 | 693 | 0.69 | 0.77 | 82 | AGS, MG |
| 4 | 700 | 0.68 | 0.76 | 77 | AGS |
| 5 | 173 | 0.67 | 0.87 | 28 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1094 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 1010 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–C · 942 Ų buried · 9 hydrogen bonds · protein-nucleic
- B–C · 128 Ų buried · 2 hydrogen bonds · protein-nucleic
- A–D · 116 Ų buried · 2 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 covalent (covalent ligand).
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 5O6D · PDBe 5O6D · UniProt P07271
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.