SMTL ID : 5n0s.1

Crystal structure of OphA-DeltaC6 mutant Y98A in complex with SAM

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

2 x SAM: S-ADENOSYLMETHIONINE(Non-covalent)

SAM.1: 22 residues within 4Å: Chain A: I.18, A.97, G.98, H.99, V.102, F.103, V.104, S.128, A.129, F.170, Q.171, Y.210, I.211, A.212, M.214, G.241, V.242, S.243, T.244 Chain B: P.398, W.399, V.400 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:A.97, A:H.99, A:A.129, A:Q.171, A:A.212, A:A.212, A:S.243 Water bridges: A:S.243 SAM.3: 22 residues within 4Å: Chain A: P.398, W.399, V.400 Chain B: I.18, A.97, G.98, H.99, V.102, F.103, V.104, S.128, A.129, F.170, Q.171, Y.210, I.211, A.212, M.214, G.241, V.242, S.243, T.244 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:A.97, B:H.99, B:H.99, B:A.129, B:Q.171, B:A.212, B:A.212, B:S.243, B:T.244 Water bridges: B:S.243

2 x MLI: MALONATE ION(Non-functional Binders)

MLI.2: 6 residues within 4Å: Chain A: K.69, N.73, Q.77 Chain B: A.301, Q.304, H.308 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.73, A:Q.77 Salt bridges: A:K.69, A:K.69 Hydrophobic interactions: B:Q.304 MLI.4: 6 residues within 4Å: Chain A: A.301, Q.304, H.308 Chain B: K.69, N.73, Q.77 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.73, B:Q.77, A:Q.304 Salt bridges: B:K.69, B:K.69 Hydrophobic interactions: A:Q.304

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Song, H. et al., A molecular mechanism for the enzymatic methylation of nitrogen atoms within peptide bonds. Sci Adv (2018)

Release Date

2018-02-14

Peptides

Peptide N-methyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Peptide N-methyltransferase