MolNFT v1 · #96712 · protein + DNA

Structure of E. COLI exonuclease I in complex with a 5CY-DT13 oligonucleotide

4JRP: “Structure of E. COLI exonuclease I in complex with a 5CY-DT13 oligonucleotide”. X-ray diffraction, 3 ligands (5CY, MG, SO4), 12 pockets (best druggability 0.83). MolNFT v1 #96712 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 4JRP
Type: protein + DNA
Length: 951 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5CY-DT13; Exodeoxyribonuclease I
EC: 3.1.11.1
UniProt: P04995
Ligands: 5CY, MG, SO4
Pockets: 12 · best druggability 0.83

Structure

x-ray diffraction · 3 distinct chains · 51% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C, D	5CY-DT13	dna	13	—	—
A	Exodeoxyribonuclease I (EC 3.1.11.1)	protein	460	50% helix, 13% strand	P04995
B	Exodeoxyribonuclease I (EC 3.1.11.1)	protein	465	52% helix, 14% strand	P04995

Ligands and binding sites

5CY · 1-(3-hydroxypropyl)-2-{(1E,3E,5E)-5-[1-(3-hydroxypropyl)-3,3-dimethyl-1,3-dihydro-2H-indol-2-ylidene]penta-1,3-dien-1-yl}-3,3-dimethyl-3H-indolium · ligand · 2 copies · chains C, D, A, B
MG · Magnesium ion · metal · chains C, A
SO4 · Sulfate ion · ion · 14 copies · chains C, A, B
GOL · Glycerol · additive · 2 copies · chains A
IPA · Isopropyl alcohol · additive · chains B

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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1003	0.83	0.84	89	SO4
2	903	0.76	0.80	81	5CY
3	789	0.76	0.81	56	SO4
4	139	0.57	0.83	20	empty
5	213	0.56	0.79	26	empty

Interfaces

5 interfaces between chains.

C–A · 1619 Å² buried · 27 hydrogen bonds · protein-nucleic
D–B · 1422 Å² buried · 18 hydrogen bonds · protein-nucleic
A–B · 1060 Å² buried · 12 hydrogen bonds · protein-protein
D–A · 439 Å² buried · 6 hydrogen bonds · protein-nucleic
C–B · 160 Å² buried · 0 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

4JRP · Structure of E. coli Exonuclease I in complex with a 5cy-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 A against A, TM-score 0.99

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 4JRP · PDBe 4JRP · UniProt P04995

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