MolNFT v1 · #176626 · protein

Structure of mod subunit of the type III restriction-modification enzyme mboiii

7DSU: “Structure of mod subunit of the type III restriction-modification enzyme mboiii”. X-ray diffraction, 1 ligand (SFG), 6 pockets (best druggability 0.71). MolNFT v1 #176626 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7DSU
Type: protein
Length: 832 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mboiii
Ligands: SFG
Pockets: 6 · best druggability 0.71

Structure

x-ray diffraction · 2 distinct chains · 39% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Mboiii	protein	412	37% helix, 19% strand	—
B	Mboiii	protein	420	42% helix, 19% strand	—

Ligands and binding sites

SFG · Sinefungin · ligand · 2 copies · chains A, B
EDO · 1,2-ethanediol · additive · chains B

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

Pockets

6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	491	0.71	0.81	61	SFG, EDO
2	655	0.70	0.78	81	empty
3	442	0.65	0.78	64	SFG
4	124	0.47	0.79	20	empty
5	138	0.47	0.78	29	empty

Interfaces

1 interface between chains.

A–B · 2401 Å² buried · 34 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 14 modified (engineered).

Compared structures

7DSU · Structure of Mod subunit of the Type III restriction-modification enzyme Mbo45V · the same entry in another collection · chain B against B, 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 7DSU · PDBe 7DSU

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