Research workbench
Crystal structure of E. COLI exonuclease I in complex with a DT13 oligonucleotide
Analyse Crystal structure of E. COLI exonuclease I in complex with a DT13… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JS5
- Type
- protein + DNA
- Length
- 949 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DT13 oligonucleotide; Exodeoxyribonuclease I
- EC
- 3.1.11.1
- UniProt
- P04995
- Ligands
- SO4
- Pockets
- 14 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | DT13 oligonucleotide | dna | 11 | — | — |
| D | DT13 oligonucleotide | dna | 10 | — | — |
| A, B | Exodeoxyribonuclease I (EC 3.1.11.1) | protein | 464 | 48% helix, 14% strand | P04995 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1089 | 0.79 | 0.81 | 100 | SO4 |
| 2 | 666 | 0.74 | 0.80 | 53 | SO4 |
| 3 | 491 | 0.70 | 0.80 | 65 | empty |
| 4 | 233 | 0.58 | 0.80 | 29 | empty |
| 5 | 209 | 0.57 | 0.79 | 27 | empty |
Interfaces
5 interfaces between chains.
- C–A · 1529 Ų buried · 20 hydrogen bonds · protein-nucleic
- D–B · 1407 Ų buried · 17 hydrogen bonds · protein-nucleic
- A–B · 1055 Ų buried · 18 hydrogen bonds · protein-protein
- D–A · 108 Ų buried · 0 hydrogen bonds · protein-nucleic
- C–B · 87 Ų buried · 0 hydrogen bonds · protein-nucleic
Compared structures
- 4JS5 · Crystal structure of E. coli Exonuclease I in complex with a dT13 oligonucleotide · the same entry in another collection · chain C against C, 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 4JS5 · PDBe 4JS5 · UniProt P04995
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