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Structure of sdai restriction endonuclease

Analyse Structure of sdai restriction endonuclease in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2IXS
Type: protein
Length: 638 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sdai restriction endonuclease
EC: 3.1.21.4
Ligands: SO4
Pockets: 7 · best druggability 0.75

Structure

x-ray diffraction · 1 distinct chain · 40% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Sdai restriction endonuclease (EC 3.1.21.4)	protein	319	40% helix, 19% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 9 copies · chains A, B
EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains A, B
TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1120	0.75	0.78	102	SO4, TRS, EPE
2	377	0.64	0.79	48	EPE
3	105	0.49	0.81	20	empty
4	115	0.40	0.75	22	empty
5	65	0.38	0.79	16	empty

Interfaces

1 interface between chains.

A–B · 400 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

2IXS · Structure of SdaI restriction endonuclease · the same entry in another collection · 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
Elsewhere: RCSB PDB 2IXS · PDBe 2IXS

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