MolNFT v1 · #96713 · protein + DNA
Crystal structure of E. COLI exonuclease I in complex with a 5CY-DA13 oligonucleotide
4JRQ: “Crystal structure of E. COLI exonuclease I in complex with a 5CY-DA13 oligonucleotide”. X-ray diffraction, 1 ligand (SO4), 11 pockets (best druggability 0.81). MolNFT v1 #96713 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 4JRQ
- Type
- protein + DNA
- Length
- 945 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5CY-DA13; Exodeoxyribonuclease I
- EC
- 3.1.11.1
- UniProt
- P04995
- Ligands
- SO4
- Pockets
- 11 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 50% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D | 5CY-DA13 | dna | 13 | — | — |
| A | Exodeoxyribonuclease I (EC 3.1.11.1) | protein | 460 | 51% helix, 15% strand | P04995 |
| B | Exodeoxyribonuclease I (EC 3.1.11.1) | protein | 459 | 50% helix, 15% strand | P04995 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 9 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1123 | 0.81 | 0.82 | 81 | SO4 |
| 2 | 936 | 0.79 | 0.81 | 61 | SO4 |
| 3 | 515 | 0.72 | 0.81 | 63 | SO4 |
| 4 | 255 | 0.60 | 0.80 | 26 | empty |
| 5 | 91 | 0.59 | 0.88 | 16 | empty |
Interfaces
5 interfaces between chains.
- D–B · 1653 Ų buried · 23 hydrogen bonds · protein-nucleic
- C–A · 1620 Ų buried · 24 hydrogen bonds · protein-nucleic
- A–B · 975 Ų buried · 13 hydrogen bonds · protein-protein
- D–A · 134 Ų buried · 2 hydrogen bonds · protein-nucleic
- C–B · 91 Ų buried · 0 hydrogen bonds · protein-nucleic
Compared structures
- 4JRQ · Crystal structure of E. coli Exonuclease I in complex with a 5cy-dA13 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 4JRQ · PDBe 4JRQ · UniProt P04995
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