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Crystal structure of probable methyltransferase from bordetella pertussis tohama I

Analyse Crystal structure of probable methyltransferase from bordetella pertussis… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3KTY
Type: protein
Length: 510 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Probable methyltransferase
UniProt: Q7VXA3
Ligands: SO4
Pockets: 3 · best druggability 0.54

Structure

x-ray diffraction · 3 distinct chains · 43% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Probable methyltransferase	protein	167	45% helix, 18% strand	Q7VXA3
B	Probable methyltransferase	protein	173	43% helix, 18% strand	Q7VXA3
C	Probable methyltransferase	protein	170	42% helix, 19% strand	Q7VXA3

Ligands and binding sites

SO4 · Sulfate ion · ion · 2 copies · chains B, C
GOL · Glycerol · additive · 2 copies · chains A, B

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

Pockets

3 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	241	0.54	0.77	29	empty
2	106	0.52	0.82	18	empty
3	97	0.48	0.81	28	empty

Interfaces

2 interfaces between chains.

B–C · 1345 Å² buried · 27 hydrogen bonds · protein-protein
A–B · 297 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 modified (engineered).

Compared structures

3KTY · Crystal Structure of Probable Methyltransferase from Bordetella pertussis Tohama I · the same entry in another collection · chain C against C, TM-score 1.00

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Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q7VXA3
Elsewhere: RCSB PDB 3KTY · PDBe 3KTY · UniProt Q7VXA3

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