MolNFT v1 · #19460 · protein

Sm endonuclease from seratia marcenscens at atomic resolution

1QL0: “Sm endonuclease from seratia marcenscens at atomic resolution”. X-ray diffraction, 1 ligand (MG), 1 pocket (best druggability 0.34). MolNFT v1 #19460 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1QL0
Type: protein
Length: 482 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
Pockets: 1 · best druggability 0.34

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	241	27% helix, 22% strand	P13717

Ligands and binding sites

MG · Magnesium ion · metal · 2 copies · chains B, A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	62	0.34	0.77	19	MG

Interfaces

1 interface between chains.

A–B · 928 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

1QL0 · Sm Endonuclease from Seratia marcenscens at atomic 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 1QL0 · PDBe 1QL0 · UniProt P13717

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