SMTL ID : 3nyq.2 (1 other biounit)

Malonyl-CoA Ligase Ternary Product Complex with Methylmalonyl-CoA and AMP bound

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.43 Å

Oligo State

homo-dimer

Ligands

2 x MCA: METHYLMALONYL-COENZYME A(Non-covalent)

MCA.1: 21 residues within 4Å: Chain A: L.203, P.204, H.207, V.208, H.209, V.250, T.252, R.256, S.281, R.303, G.305, M.306, T.307, M.311, K.410, G.412, G.413, Y.414, L.444, R.481 Ligands: AMP.2 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:V.208, A:V.250, A:T.252, A:Y.414 Hydrogen bonds: A:V.208, A:H.209, A:S.281, A:S.281, A:G.305, A:G.412, A:G.413 Water bridges: A:R.481, A:R.481, A:R.481, A:R.481 Salt bridges: A:H.209, A:R.256, A:R.303, A:R.481 MCA.6: 21 residues within 4Å: Chain B: L.203, P.204, H.207, V.208, H.209, V.250, T.252, R.256, S.281, R.303, G.305, M.306, T.307, M.311, K.410, G.412, G.413, Y.414, L.444, R.481 Ligands: AMP.7 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:V.208, B:V.250, B:T.252, B:Y.414 Hydrogen bonds: B:V.208, B:H.209, B:S.281, B:S.281, B:G.305, B:G.412, B:G.413 Water bridges: B:Y.414, B:R.481, B:R.481, B:R.481, B:R.481 Salt bridges: B:H.209, B:R.256, B:R.303, B:R.481

2 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.2: 17 residues within 4Å: Chain A: T.163, S.281, A.282, A.283, E.302, R.303, Y.304, G.305, M.306, T.307, V.326, D.388, I.400, L.408, K.410, K.415 Ligands: MCA.1 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:T.163, A:S.281, A:E.302, A:R.303, A:G.305, A:T.307, A:T.307, A:D.388, A:K.410 Water bridges: A:T.163, A:L.284, A:T.307, A:D.388, A:K.415, A:K.415 Salt bridges: A:K.410, A:K.415 pi-Stacking: A:Y.304 AMP.7: 17 residues within 4Å: Chain B: T.163, S.281, A.282, A.283, E.302, R.303, Y.304, G.305, M.306, T.307, V.326, D.388, I.400, L.408, K.410, K.415 Ligands: MCA.6 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:T.163, B:T.163, B:S.281, B:E.302, B:E.302, B:R.303, B:G.305, B:T.307, B:T.307, B:T.307, B:D.388, B:K.410 Water bridges: B:L.284, B:K.415, B:K.415 Salt bridges: B:K.410, B:K.415 pi-Stacking: B:Y.304

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 4 residues within 4Å: Chain A: F.44, R.47, A.78, M.79 Ligand excluded by PLIP CL.4: 4 residues within 4Å: Chain A: N.99, A.475, P.476, H.477 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain B: F.44, R.47, A.78, M.79 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain B: N.99, A.475, P.476, H.477 Ligand excluded by PLIP

2 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 1 residues within 4Å: Chain B: E.351 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:E.351, H2O.14, H2O.14, H2O.14, H2O.14, H2O.14 MG.10: 1 residues within 4Å: Chain A: E.351 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:E.351, H2O.29, H2O.29, H2O.29, H2O.29, H2O.29

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hughes, A.J. et al., Enzymatic Extender Unit Generation for In Vitro Polyketide Synthase Reactions: Structural and Functional Showcasing of Streptomyces coelicolor MatB. Chem.Biol. (2011)

Release Date

2011-03-30

Peptides

Malonyl-CoA Ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Malonyl-CoA Ligase

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