SMTL ID : 6lkc.1

Crystal structure of PfaD from Shewanella piezotolerans in complex with FMN

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 21 residues within 4Å: Chain A: G.146, A.147, M.148, A.149, A.173, N.199, S.228, K.262, E.310, D.312, S.313, G.314, G.352, G.353, T.373, G.374, S.375, Q.378, W.521, A.525 Ligands: CA.2 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:M.148, A:W.521, A:W.521 Hydrogen bonds: A:A.147, A:A.149, A:N.199, A:N.199, A:S.228, A:K.262, A:K.262, A:E.310, A:G.314, A:G.353, A:G.374, A:S.375 Water bridges: A:H.316, A:G.352, A:V.354 FMN.4: 20 residues within 4Å: Chain B: G.146, A.147, M.148, A.149, A.173, N.199, S.228, K.262, E.310, D.312, S.313, G.314, G.352, G.353, G.374, S.375, Q.378, W.521, A.525 Ligands: CA.5 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:M.148, B:W.521, B:W.521 Hydrogen bonds: B:A.147, B:A.149, B:N.199, B:N.199, B:S.228, B:K.262, B:K.262, B:G.314, B:G.353, B:G.374, B:S.375, B:S.375 Water bridges: B:G.352, B:V.354

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: E.310, S.313, G.314, H.316 Ligands: FMN.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.310, A:H.316, H2O.7 CA.5: 5 residues within 4Å: Chain B: E.310, S.313, G.314, H.316 Ligands: FMN.4 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.310, B:H.316, H2O.17

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: S.127, L.128, G.129, F.364, N.365 Chain B: N.564 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.129, A:N.365, B:N.564 Water bridges: A:F.364, A:A.368, A:N.561, B:N.564 GOL.6: 9 residues within 4Å: Chain A: N.564, T.567, S.568 Chain B: S.127, L.128, G.129, F.364, N.365, N.561 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.129, B:F.364, B:N.365, B:N.561, B:N.561 GOL.7: 4 residues within 4Å: Chain A: A.399 Chain B: R.265, T.266, R.320 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.265, B:T.266, B:T.266, B:R.320, B:R.320

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, M. et al., Structural Insights into the Trans -Acting Enoyl Reductase in the Biosynthesis of Long-Chain Polyunsaturated Fatty Acids in Shewanella piezotolerans . J.Agric.Food Chem. (2021)

Release Date

2020-12-23

Peptides

Polyunsaturated fatty acid synthase PfaD: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Polyunsaturated fatty acid synthase PfaD