MolNFT v1 · #89931 · protein

X-ray structure of the serratia marcescens endonuclease at 0.95 a resolution

4E3Y: “X-ray structure of the serratia marcescens endonuclease at 0.95 a resolution”. X-ray diffraction, 2 ligands (MG, SO4), 2 pockets (best druggability 0.36). MolNFT v1 #89931 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 4E3Y
Type: protein
Length: 480 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nuclease
EC: 3.1.30.2
UniProt: P13717
Ligands: MG, SO4
Pockets: 2 · best druggability 0.36

Structure

x-ray diffraction · 1 distinct chain · 27% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Nuclease (EC 3.1.30.2)	protein	240	27% helix, 22% strand	P13717

Ligands and binding sites

MG · Magnesium ion · metal · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 2 copies · chains B
EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
PEG · Di(hydroxyethyl)ether · additive · chains A
GOL · Glycerol · additive · chains B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	91	0.36	0.75	20	MG
2	60	0.33	0.77	20	MG, SO4

Interfaces

1 interface between chains.

A–B · 868 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

4E3Y · X-ray structure of the Serratia marcescens endonuclease at 0.95 A resolution · the same entry in another collection · chain A against A, TM-score 1.00
P13717 · AlphaFold monomer V2.0 prediction for nuclease (P13717) · a predicted model of the same protein · chain A against A, TM-score 1.00

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 P13717
Elsewhere: RCSB PDB 4E3Y · PDBe 4E3Y · UniProt P13717

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