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Sm endonuclease from seratia marcenscens at 1.1 a resolution

Analyse Sm endonuclease from seratia marcenscens at 1.1 a resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1G8T
Type: protein
Length: 482 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nuclease SM2 isoform
EC: 3.1.30.2
UniProt: P13717
Ligands: MG, SO4
Pockets: 2 · best druggability 0.34

Structure

x-ray diffraction · 1 distinct chain · 28% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Nuclease SM2 isoform (EC 3.1.30.2)	protein	241	28% helix, 22% strand	P13717

Ligands and binding sites

MG · Magnesium ion · metal · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 4 copies · chains A, 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	69	0.34	0.76	21	SO4, MG
2	62	0.33	0.76	16	SO4, MG

Interfaces

1 interface between chains.

A–B · 916 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

1G8T · Sm endonuclease from seratia marcenscens at 1.1 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 1G8T · PDBe 1G8T · UniProt P13717

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