SMTL ID : 3i58.1

Crystal structure of an O-methyltransferase (NcsB1) from neocarzinostatin biosynthesis in complex with S-adenosyl-L-homocysteine (SAH) and 2-hydroxy-7-methoxy-5-methyl naphthoic acid (NA)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.69 Å

Oligo State

homo-dimer

Ligands

2 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.1: 19 residues within 4Å: Chain A: W.133, F.146, M.150, H.153, L.154, G.177, G.178, G.179, D.200, L.201, P.204, G.226, S.227, F.228, F.229, S.242, A.243, D.247, W.248 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:G.177, A:G.179, A:L.201, A:S.227, A:F.228, A:S.242 Water bridges: A:S.242, A:S.242, A:S.242 Salt bridges: A:H.153 pi-Stacking: A:W.133, A:W.133, A:F.228 SAH.4: 19 residues within 4Å: Chain B: W.133, F.146, M.150, H.153, L.154, G.177, G.178, G.179, D.200, L.201, P.204, G.226, S.227, F.228, F.229, S.242, A.243, D.247, W.248 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:G.179, B:L.201, B:S.227, B:F.228, B:S.242, B:S.242 Water bridges: B:S.242, B:S.242 Salt bridges: B:H.153 pi-Stacking: B:W.133, B:W.133, B:F.228

2 x 7NA: 2-hydroxy-7-methoxy-5-methyl naphthoic acid(Non-covalent)

7NA.2: 12 residues within 4Å: Chain A: W.96, V.103, M.150, H.153, A.243, H.246, M.286, R.289, M.290, Y.293, F.294 Chain B: R.11 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:V.103, A:V.103, A:Y.293, A:F.294 Water bridges: A:R.289, B:R.11 Hydrogen bonds: B:R.11 Salt bridges: B:R.11 7NA.5: 13 residues within 4Å: Chain A: R.11 Chain B: W.96, V.103, F.146, M.150, H.153, A.243, H.246, M.286, R.289, M.290, Y.293, F.294 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:V.103, B:V.103, B:F.146, B:Y.293, B:F.294 Hydrogen bonds: A:R.11, A:R.11

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 2 residues within 4Å: Chain A: G.219, R.220 No protein-ligand interaction detected (PLIP) GOL.6: 1 residues within 4Å: Chain B: G.219 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cooke, H.A. et al., Molecular basis of substrate promiscuity for the SAM-dependent O-methyltransferase NcsB1, involved in the biosynthesis of the enediyne antitumor antibiotic neocarzinostatin. Biochemistry (2009)

Release Date

2009-09-01

Peptides

O-methyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

O-methyltransferase

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