Research workbench
Crystal structure of E. coli Exonuclease I in complex with a dA16 oligonucleotide
Analyse Crystal structure of E. coli Exonuclease I in complex with a dA16… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JS4
- Type
- protein + DNA
- Length
- 958 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.1
- Source
- Escherichia coli; SYNTHETIC CONSTRUCT
- Molecule
- dT16 oligonucleotide; Exodeoxyribonuclease I
- EC
- 3.1.11.1
- UniProt
- P04995
- Ligands
- SO4
- Pockets
- 12 · best druggability 0.80
Structure
x-ray diffraction · resolution 3.1 · 4 distinct chains · 49% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | dT16 oligonucleotide | dna | 15 | — | — |
| D | dT16 oligonucleotide | dna | 14 | — | — |
| A | Exodeoxyribonuclease I (EC 3.1.11.1) | protein | 468 | 48% helix, 15% strand | P04995 |
| B | Exodeoxyribonuclease I (EC 3.1.11.1) | protein | 461 | 50% helix, 14% strand | P04995 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1066 | 0.80 | 0.82 | 86 | SO4 |
| 2 | 1162 | 0.79 | 0.81 | 87 | empty |
| 3 | 484 | 0.73 | 0.83 | 59 | SO4 |
| 4 | 321 | 0.68 | 0.83 | 34 | empty |
| 5 | 136 | 0.51 | 0.80 | 32 | empty |
Interfaces
5 interfaces between chains.
- C–A · 1869 Ų buried · 24 hydrogen bonds · protein-nucleic
- D–B · 1715 Ų buried · 25 hydrogen bonds · protein-nucleic
- A–B · 975 Ų buried · 11 hydrogen bonds · protein-protein
- D–A · 183 Ų buried · 0 hydrogen bonds · protein-nucleic
- C–B · 169 Ų buried · 0 hydrogen bonds · protein-nucleic
Compared structures
- 4JS4 · Crystal structure of E. COLI exonuclease I in complex with a DA16 oligonucleotide · the same entry in another collection · chain A against A, TM-score 1.00
- P04995 · AlphaFold monomer V2.0 prediction for exodeoxyribonuclease I (P04995) · a predicted model of the same protein · chain B 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 P04995
- Elsewhere: RCSB PDB 4JS4 · PDBe 4JS4 · UniProt P04995
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