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The structure of miab with pentasulfide bridge

Analyse The structure of miab with pentasulfide bridge in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7MJZ
Type: protein
Length: 444 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: TRNA-2-methylthio-N(6)-dimethylallyladenosine synthase
EC: 2.8.4.3
UniProt: A0A174GYG1
Ligands: SF4, PS5, NA
Pockets: 2 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	TRNA-2-methylthio-N(6)-dimethylallyladenosine synthase (EC 2.8.4.3)	protein	444	38% helix, 24% strand	A0A174GYG1

Ligands and binding sites

SF4 · Iron/sulfur cluster · ligand · 2 copies · chains A
PS5 · Pentasulfide-sulfur · ligand · chains A
NA · Sodium ion · metal · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	613	0.77	0.83	55	SF4, PS5
2	61	0.31	0.76	14	empty

Compared structures

7MJZ · The structure of MiaB with pentasulfide bridge · 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
Every structure of UniProt A0A174GYG1
Elsewhere: RCSB PDB 7MJZ · PDBe 7MJZ · UniProt A0A174GYG1

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