Research workbench
Structural insights into 5' flap DNA unwinding and incision by the human FAN1 dimer
Analyse Structural insights into 5' flap DNA unwinding and incision by the human FAN1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4REB
- Type
- protein + DNA
- Length
- 1,189 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fanconi-associated nuclease 1; DNA (5'-D(P*GP*TP*GP*GP*CP*GP*AP*GP*C)-3'); DNA (5'…
- EC
- 3.1.21.-, 3.1.4.1
- UniProt
- Q9Y2M0
- Ligands
- SM
- Pockets
- 17 · best druggability 0.66
Structure
x-ray diffraction · 5 distinct chains · 60% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fanconi-associated nuclease 1 (EC 3.1.21.-, 3.1.4.1) | protein | 566 | 61% helix, 7% strand | Q9Y2M0 |
| H | Fanconi-associated nuclease 1 (EC 3.1.21.-, 3.1.4.1) | protein | 584 | 59% helix, 6% strand | Q9Y2M0 |
| D | DNA (5'-D(P*GP*TP*GP*GP*CP*GP*AP*GP*C)-3') | dna | 9 | — | — |
| E | DNA (5'- D(P*CP*GP*TP*GP*GP*CP*GP*AP*GP*CP*GP*CP*TP*CP*GP*CP*CP*AP*CP*G)-3') | dna | 20 | — | — |
| F | DNA (5'-D(P*GP*CP*TP*CP*GP*CP*CP*AP*CP*G)-3') | dna | 10 | — | — |
Ligands and binding sites
- SM · Samarium (III) ion · metal · 2 copies · chains A, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 564 | 0.66 | 0.77 | 59 | empty |
| 2 | 490 | 0.65 | 0.77 | 41 | empty |
| 3 | 476 | 0.61 | 0.75 | 40 | empty |
| 4 | 486 | 0.59 | 0.75 | 42 | empty |
| 5 | 183 | 0.59 | 0.81 | 34 | empty |
Interfaces
7 interfaces between chains.
- E–F · 496 Ų buried · 53 hydrogen bonds · nucleic-nucleic
- A–H · 473 Ų buried · 4 hydrogen bonds · protein-protein
- D–E · 451 Ų buried · 44 hydrogen bonds · nucleic-nucleic
- A–F · 253 Ų buried · 5 hydrogen bonds · protein-nucleic
- A–E · 143 Ų buried · 1 hydrogen bond · protein-nucleic
Compared structures
- 4REB · Structural Insights into 5' Flap DNA Unwinding and Incision by the Human FAN1 Dimer · the same entry in another collection · chain E against E, TM-score 1.00
- Q9Y2M0 · AlphaFold monomer V2.0 prediction for fanconi-associated nuclease 1 (Q9Y2M0) · a predicted model of the same protein · chain H against A, TM-score 0.98
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 4REB · PDBe 4REB · UniProt Q9Y2M0
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