Research workbench
FAN1 nuclease bound to 5' phosphorylated P(DT)/3'(DT-dt-dt-dt-dt-dt- dt-dt) double flap DNA
Analyse FAN1 nuclease bound to 5' phosphorylated P(DT)/3'(DT-dt-dt-dt-dt-dt- dt-dt)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RI9
- Type
- protein + DNA
- Length
- 1,314 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fanconi-associated nuclease 1; DNA (5'-D(P*TP*AP*GP*CP*CP*AP*CP*GP*CP*CP*T)-3'); DNA (5'…
- EC
- 3.1.21.-, 3.1.4.1
- UniProt
- Q9Y2M0
- Ligands
- BA
- Pockets
- 19 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 59% helix, 8% 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 | 59% helix, 8% strand | Q9Y2M0 |
| S, W | DNA (5'-D(P*TP*AP*GP*CP*CP*AP*CP*GP*CP*CP*T)-3') | dna | 11 | — | — |
| U, Z | DNA (5'- D(P*AP*GP*AP*CP*TP*CP*CP*TP*CP*TP*TP*TP*TP*TP*TP*TP*T)-3') | dna | 12 | — | — |
| V, X | DNA (5'-D(P*GP*CP*TP*GP*AP*GP*GP*AP*GP*TP*CP*T)-3') | dna | 12 | — | — |
| Y, T | DNA (5'-D(*TP*TP*TP*TP*TP*TP*GP*AP*GP*GP*CP*GP*TP*G)-3') | dna | 7 | — | — |
Ligands and binding sites
- BA · Barium ion · metal · 2 copies · chains A, S, B, W
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 | 952 | 0.83 | 0.85 | 57 | empty |
| 2 | 1117 | 0.83 | 0.84 | 57 | empty |
| 3 | 505 | 0.76 | 0.84 | 54 | empty |
| 4 | 461 | 0.75 | 0.84 | 45 | empty |
| 5 | 470 | 0.68 | 0.80 | 33 | empty |
Interfaces
17 interfaces between chains.
- B–W · 700 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–S · 608 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–B · 591 Ų buried · 2 hydrogen bonds · protein-protein
- A–Z · 477 Ų buried · 16 hydrogen bonds · protein-nucleic
- B–U · 468 Ų buried · 15 hydrogen bonds · protein-nucleic
Compared structures
- 4RI9 · FAN1 Nuclease bound to 5' phosphorylated p(dT)/3'(dT-dT-dT-dT-dT-dT-dT-dT) double flap DNA · the same entry in another collection · chain T against T, TM-score 1.00
- Q9Y2M0 · AlphaFold monomer V2.0 prediction for fanconi-associated nuclease 1 (Q9Y2M0) · a predicted model of the same protein · chain B against A, TM-score 0.94
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 4RI9 · PDBe 4RI9 · UniProt Q9Y2M0
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