MolNFT v1 · #105746 · protein + DNA
Structural insights into 5' flap DNA unwinding and incision by the human FAN1 dimer
4REB · Fanconi-associated nuclease 1: “Structural insights into 5' flap DNA unwinding and incision by the human FAN1 dimer”. X-ray diffraction, 1 ligand (SM), 17 pockets (best druggability 0.66). MolNFT v1 #105746 on GenesisL1: 3D…
- 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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