Research workbench
FAN1 nuclease bound to 5' phosphorylated P(DT) single flap DNA
Analyse FAN1 nuclease bound to 5' phosphorylated P(DT) single flap DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RIB
- Type
- protein + DNA
- Length
- 1,321 residues
- Chains
- 8
- 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*TP*AP*GP*AP*CP*T…
- EC
- 3.1.21.-, 3.1.4.1
- UniProt
- Q9Y2M0
- Ligands
- CA
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 5 distinct chains · 57% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fanconi-associated nuclease 1 (EC 3.1.21.-, 3.1.4.1) | protein | 615 | 58% helix, 7% strand | Q9Y2M0 |
| B | Fanconi-associated nuclease 1 (EC 3.1.21.-, 3.1.4.1) | protein | 628 | 55% helix, 8% strand | Q9Y2M0 |
| X, U | DNA (5'- D(P*TP*AP*GP*CP*CP*AP*CP*GP*CP*CP*TP*AP*GP*AP*CP*TP*CP*CP*TP*C)-3') | dna | 20 | — | — |
| Y, V | DNA (5'-D(*GP*CP*TP*GP*AP*GP*GP*AP*GP*TP*CP*T)-3') | dna | 12 | — | — |
| Z, W | DNA (5'-D(*TP*TP*TP*TP*TP*TP*GP*AP*GP*GP*CP*GP*TP*G)-3') | dna | 7 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, U, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1109 | 0.82 | 0.84 | 49 | empty |
| 2 | 646 | 0.80 | 0.85 | 59 | empty |
| 3 | 709 | 0.73 | 0.79 | 75 | empty |
| 4 | 63 | 0.70 | 0.96 | 20 | empty |
| 5 | 56 | 0.69 | 0.97 | 19 | empty |
Interfaces
17 interfaces between chains.
- A–U · 884 Ų buried · 13 hydrogen bonds · protein-nucleic
- X–Y · 400 Ų buried · 39 hydrogen bonds · nucleic-nucleic
- U–V · 400 Ų buried · 40 hydrogen bonds · nucleic-nucleic
- A–W · 384 Ų buried · 13 hydrogen bonds · protein-nucleic
- U–W · 348 Ų buried · 35 hydrogen bonds · nucleic-nucleic
Compared structures
- 4RIB · FAN1 Nuclease bound to 5' phosphorylated p(dT) single flap DNA · the same entry in another collection · chain W against W, 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 0.94
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 4RIB · PDBe 4RIB · UniProt Q9Y2M0
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