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Crystal structure of opha-DELTAC6 mutant W400A in complex with SAM

Analyse Crystal structure of opha-DELTAC6 mutant W400A 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: 5N4I
Type: protein
Length: 393 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Peptide N-methyltransferase
Ligands: SAM, BCT, SCN
Pockets: 3 · best druggability 0.75

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Peptide N-methyltransferase	protein	393	38% helix, 14% strand	—

Ligands and binding sites

SAM · S-adenosylmethionine · ligand · chains A
BCT · Bicarbonate ion · ligand · chains A
SCN · Thiocyanate ion · ion · 4 copies · chains A
GOL · Glycerol · additive · chains A
MLI · Malonate ion · additive · chains A

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

Pockets

3 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	456	0.75	0.84	56	SAM
2	179	0.50	0.77	31	empty
3	67	0.38	0.78	15	empty

Modifications

Observed in the structure: 2 modified (methylation, nonstandard).

Compared structures

5N4I · Crystal structure of OphA-DeltaC6 mutant W400A 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
Elsewhere: RCSB PDB 5N4I · PDBe 5N4I

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