Research workbench
FAN1 nuclease bound to 5' phosphorylated P(DG)/3'(DT-dt-dt-dt) double flap DNA
Analyse FAN1 nuclease bound to 5' phosphorylated P(DG)/3'(DT-dt-dt-dt) double flap DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RI8
- Type
- protein + DNA
- Length
- 1,312 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fanconi-associated nuclease 1; DNA (5'-D(*TP*TP*TP*GP*AP*GP*GP*AP*GP*TP*CP*TP*TP*T)-3')…
- EC
- 3.1.21.-, 3.1.4.1
- UniProt
- Q9Y2M0
- Ligands
- CA
- Pockets
- 19 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 58% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Fanconi-associated nuclease 1 (EC 3.1.21.-, 3.1.4.1) | protein | 615 | 58% helix, 7% strand | Q9Y2M0 |
| E, H | DNA (5'-D(*TP*TP*TP*GP*AP*GP*GP*AP*GP*TP*CP*TP*TP*T)-3') | dna | 14 | — | — |
| F, I | DNA (5'-D(P*GP*AP*GP*GP*CP*GP*TP*G)-3') | dna | 8 | — | — |
| G, J | DNA (5'- D(*AP*AP*CP*AP*CP*GP*CP*CP*TP*AP*GP*AP*CP*TP*CP*CP*TP*CP*A)-3') | dna | 19 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, F, B, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1084 | 0.86 | 0.87 | 85 | empty |
| 2 | 883 | 0.81 | 0.84 | 48 | empty |
| 3 | 451 | 0.77 | 0.85 | 42 | empty |
| 4 | 545 | 0.69 | 0.79 | 36 | empty |
| 5 | 533 | 0.68 | 0.79 | 33 | empty |
Interfaces
11 interfaces between chains.
- B–J · 660 Ų buried · 18 hydrogen bonds · protein-nucleic
- A–G · 636 Ų buried · 20 hydrogen bonds · protein-nucleic
- A–F · 610 Ų buried · 15 hydrogen bonds · protein-nucleic
- B–I · 594 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–B · 560 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4RI8 · FAN1 Nuclease bound to 5' phosphorylated p(dG)/3'(dT-dT-dT-dT) double flap DNA · the same entry in another collection · chain J against J, TM-score 1.00
- Q9Y2M0 · AlphaFold monomer V2.0 prediction for fanconi-associated nuclease 1 (Q9Y2M0) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q9Y2M0
- Elsewhere: RCSB PDB 4RI8 · PDBe 4RI8 · UniProt Q9Y2M0
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