SMTL ID : 2qyo.1

Crystal structure of isoflavone O-methyltransferase homolog in complex with biochanin A and SAH

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

13 x K: POTASSIUM ION(Non-covalent)(Non-functional Binders)

K.1: 4 residues within 4Å: Chain A: H.262, D.293, M.294, E.323 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.262, A:D.293, A:E.323, A:E.323, H2O.1 K.2: 2 residues within 4Å: Chain A: R.8, K.9 No protein-ligand interaction detected (PLIP) K.3: 2 residues within 4Å: Chain A: A.100, L.101 No protein-ligand interaction detected (PLIP) K.4: 3 residues within 4Å: Chain A: G.111, C.115, P.118 No protein-ligand interaction detected (PLIP) K.5: 3 residues within 4Å: Chain A: T.145, D.154, L.155 No protein-ligand interaction detected (PLIP) K.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) K.7: 3 residues within 4Å: Chain A: N.325, E.326, E.327 No protein-ligand interaction detected (PLIP) K.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) K.11: 4 residues within 4Å: Chain A: R.76 Chain B: N.297, E.298, N.325 No protein-ligand interaction detected (PLIP) K.12: 2 residues within 4Å: Chain B: T.145, L.155 No protein-ligand interaction detected (PLIP) K.13: 4 residues within 4Å: Chain B: H.262, D.293, M.294, E.323 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.262, B:D.293, B:E.323, B:E.323, H2O.4 K.14: 2 residues within 4Å: Chain B: F.158, N.162 No protein-ligand interaction detected (PLIP) K.15: 2 residues within 4Å: Chain A: H.133 Chain B: S.129 No protein-ligand interaction detected (PLIP)

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

SAH.9: 15 residues within 4Å: Chain A: G.201, G.203, T.207, D.224, R.225, V.228, G.243, D.244, M.245, F.246, K.258, A.259, V.260, D.263, W.264 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:A.259 Hydrogen bonds: A:G.203, A:R.225, A:R.225, A:D.244, A:M.245, A:K.258 Water bridges: A:K.258 Salt bridges: A:K.258 SAH.16: 12 residues within 4Å: Chain B: G.201, G.203, T.207, D.224, R.225, V.228, D.244, M.245, F.246, K.258, A.259, W.264 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:G.203, B:T.207, B:R.225, B:R.225, B:D.244, B:M.245, B:K.258 Water bridges: B:K.258 Salt bridges: B:K.258

2 x QSO: 5,7-dihydroxy-3-(4-methoxyphenyl)-4H-chromen-4-one(Non-covalent)

QSO.10: 14 residues within 4Å: Chain A: C.122, V.123, L.128, S.129, F.132, F.147, L.155, Y.165, H.262, D.263, T.315, I.316, V.319 Chain B: Y.25 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.128, A:F.132, A:V.319 Hydrogen bonds: A:V.123 pi-Stacking: A:F.147 QSO.17: 9 residues within 4Å: Chain A: Y.25 Chain B: V.123, L.128, S.129, F.132, F.147, H.262, I.316, V.319 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.128, B:F.132, B:V.319, A:Y.25 pi-Stacking: B:F.147

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, C. et al., Crystal structures of Medicago truncatula isoflavone O-methyltransferase reveal conserved surface binding motifs critical for enzymatic activity. To be Published

Release Date

2008-08-26

Peptides

O-methyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

O-methyltransferase