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Crystal structure of tnmh in complex with SAM

Analyse Crystal structure of tnmh in complex with SAM in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6CLX
Type: protein
Length: 682 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: O-methyltransferase
UniProt: A0A125SA05
Ligands: SAM
Pockets: 5 · best druggability 0.80

Structure

x-ray diffraction · 2 distinct chains · 51% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	O-methyltransferase	protein	340	52% helix, 14% strand	A0A125SA05
B	O-methyltransferase	protein	342	51% helix, 14% strand	A0A125SA05

Ligands and binding sites

SAM · S-adenosylmethionine · ligand · 2 copies · chains A, B

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

Pockets

5 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	999	0.80	0.81	87	SAM
2	819	0.75	0.79	68	empty
3	187	0.72	0.89	29	SAM
4	87	0.48	0.82	25	empty
5	90	0.31	0.72	23	empty

Interfaces

1 interface between chains.

A–B · 3416 Å² buried · 29 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 modified (engineered).

Compared structures

6CLX · Crystal structure of TnmH in complex with SAM · 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 A0A125SA05
Elsewhere: RCSB PDB 6CLX · PDBe 6CLX · UniProt A0A125SA05

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