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Crystal structure of opha-DELTAC6 mutant R72A in complex with SAM

Analyse Crystal structure of opha-DELTAC6 mutant R72A 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: 5N0W
Type: protein
Length: 784 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Peptide N-methyltransferase
Ligands: SAM
Pockets: 6 · best druggability 0.82

Structure

x-ray diffraction · 2 distinct chains · 38% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Peptide N-methyltransferase	protein	397	38% helix, 14% strand	—
B	Peptide N-methyltransferase	protein	387	39% helix, 15% strand	—

Ligands and binding sites

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

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

Pockets

6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	164	0.82	0.97	37	SAM, GOL
2	464	0.80	0.88	65	SAM
3	810	0.78	0.82	101	empty
4	621	0.75	0.81	94	empty
5	223	0.62	0.82	32	empty

Interfaces

1 interface between chains.

A–B · 7558 Å² buried · 93 hydrogen bonds · protein-protein

Compared structures

5N0W · Crystal structure of OphA-DeltaC6 mutant R72A in complex with SAM · the same entry in another collection · chain B against B, 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 5N0W · PDBe 5N0W

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