Research workbench
FAN1 nuclease bound to 5' phosphorylated nicked DNA
Analyse FAN1 nuclease bound to 5' phosphorylated nicked DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RIA
- Type
- protein + DNA
- Length
- 1,302 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fanconi-associated nuclease 1; DNA (5'-D(P*AP*GP*CP*CP*AP*CP*GP*CP*CP*T)-3'); DNA…
- 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 · 57% 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 | 613 | 57% helix, 8% strand | Q9Y2M0 |
| F, L | DNA (5'-D(P*AP*GP*CP*CP*AP*CP*GP*CP*CP*T)-3') | dna | 10 | — | — |
| K, I | DNA (5'-D(P*AP*GP*AP*CP*TP*CP*CP*TP*C)-3') | dna | 9 | — | — |
| G, J | DNA (5'-D(*TP*TP*TP*TP*TP*TP*G*AP*GP*GP*CP*GP*TP*G)-3') | dna | 7 | — | — |
| E, H | DNA (5'-D(P*GP*CP*TP*GP*AP*GP*GP*AP*GP*TP*CP*T)-3') | dna | 12 | — | — |
Ligands and binding sites
- BA · Barium ion · metal · 2 copies · chains A, B
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 | 722 | 0.83 | 0.87 | 53 | BA |
| 2 | 661 | 0.82 | 0.87 | 48 | empty |
| 3 | 426 | 0.79 | 0.87 | 53 | empty |
| 4 | 69 | 0.73 | 0.97 | 18 | empty |
| 5 | 515 | 0.72 | 0.81 | 54 | empty |
Interfaces
18 interfaces between chains.
- K–E · 391 Ų buried · 42 hydrogen bonds · nucleic-nucleic
- I–H · 390 Ų buried · 39 hydrogen bonds · nucleic-nucleic
- A–G · 388 Ų buried · 14 hydrogen bonds · protein-nucleic
- B–J · 381 Ų buried · 12 hydrogen bonds · protein-nucleic
- A–E · 381 Ų buried · 10 hydrogen bonds · protein-nucleic
Compared structures
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 4RIA · PDBe 4RIA · UniProt Q9Y2M0
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