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

Analyse Crystal structure of opha-DELTAC6 mutant W400A in complex with sinefungin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5OUF
Type: protein
Length: 389 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Opha peptide N-methyltransferase
Ligands: SFG, BCT, SCN
Pockets: 3 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Opha peptide N-methyltransferase	protein	389	39% helix, 14% strand	—

Ligands and binding sites

SFG · Sinefungin · ligand · chains A
BCT · Bicarbonate ion · ligand · chains A
SCN · Thiocyanate ion · ion · 4 copies · 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	441	0.77	0.85	50	SFG
2	153	0.49	0.78	18	empty
3	207	0.48	0.75	28	empty

Modifications

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

Compared structures

5OUF · Crystal structure of OphA-DeltaC6 mutant W400A in complex with Sinefungin · 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 5OUF · PDBe 5OUF

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