Research workbench
Exonuclease X in complex with 12BP blunt-ended dsdna
Analyse Exonuclease X in complex with 12BP blunt-ended dsdna in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4FZY
- Type
- protein + DNA
- Length
- 356 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*TP*GP*TP*AP*GP*AP*TP*TP*CP*GP*AP*G)-3'); Exodeoxyribonuclease 10; DNA…
- EC
- 3.1.11.-
- UniProt
- P0AEK0
- Ligands
- NA
- Pockets
- 3 · best druggability 0.62
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | DNA (5'-D(*TP*GP*TP*AP*GP*AP*TP*TP*CP*GP*AP*G)-3') | dna | 11 | — | — |
| A | Exodeoxyribonuclease 10 (EC 3.1.11.-) | protein | 167 | 38% helix, 22% strand | P0AEK0 |
| D | DNA (5'-D(P*CP*TP*CP*GP*AP*AP*TP*CP*TP*AP*CP*A)-3') | dna | 12 | — | — |
| B | Exodeoxyribonuclease 10 (EC 3.1.11.-) | protein | 166 | 41% helix, 20% strand | P0AEK0 |
Ligands and binding sites
- NA · Sodium ion · metal · 4 copies · chains C, A, D, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 185 | 0.62 | 0.84 | 27 | empty |
| 2 | 128 | 0.58 | 0.84 | 23 | empty |
| 3 | 112 | 0.37 | 0.75 | 20 | empty |
Interfaces
5 interfaces between chains.
- D–B · 560 Ų buried · 8 hydrogen bonds · protein-nucleic
- C–A · 556 Ų buried · 8 hydrogen bonds · protein-nucleic
- C–D · 476 Ų buried · 35 hydrogen bonds · nucleic-nucleic
- C–B · 293 Ų buried · 4 hydrogen bonds · protein-nucleic
- A–D · 261 Ų buried · 2 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 P0AEK0
- Elsewhere: RCSB PDB 4FZY · PDBe 4FZY · UniProt P0AEK0
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