Research workbench
A nuclease-DNA complex form 3
Analyse A nuclease-DNA complex form 3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4REC
- Type
- protein + DNA
- Length
- 633 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fanconi-associated nuclease 1; DNA (40-mer)
- EC
- 3.1.21.-, 3.1.4.1
- UniProt
- Q9Y2M0
- Ligands
- IOD
- Pockets
- 7 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 59% 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 | 593 | 59% helix, 6% strand | Q9Y2M0 |
| B | DNA (40-mer) | dna | 40 | — | — |
Ligands and binding sites
- IOD · Iodide ion · ion · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 699 | 0.70 | 0.77 | 37 | empty |
| 2 | 546 | 0.67 | 0.78 | 55 | IOD |
| 3 | 718 | 0.67 | 0.76 | 36 | empty |
| 4 | 247 | 0.64 | 0.82 | 35 | empty |
| 5 | 233 | 0.49 | 0.75 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 613 Ų buried · 12 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 4REC · PDBe 4REC · UniProt Q9Y2M0
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