SMTL ID : 6z5o.1

CRYSTAL STRUCTURE OF RAT PEROXISOMAL MULTIFUNCTIONAL ENZYME TYPE-1 (RPMFE1) COMPLEXED WITH COENZYME-A AND OXIDISED NICOTINAMIDE ADENINE DINUCLEOTIDE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

1 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.1: 23 residues within 4Å: Chain A: L.322, G.323, L.324, G.325, T.326, M.327, E.346, S.347, D.348, Q.351, A.400, V.401, F.402, E.403, L.407, K.408, V.411, N.428, T.429, S.430, H.451, F.452, S.454 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:G.325, A:T.326, A:M.327, A:S.347, A:S.347, A:Q.351, A:K.408, A:K.408, A:N.428, A:S.430 Water bridges: A:T.326, A:G.328, A:E.403, A:E.403, A:E.403, A:K.410, A:S.454 pi-Stacking: A:F.402

5 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 4 residues within 4Å: Chain A: P.211, I.212, E.213, R.216 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:I.212, A:E.213 Water bridges: A:R.216, A:R.216 Salt bridges: A:R.216 SO4.3: 1 residues within 4Å: Chain A: R.719 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.719 SO4.4: 3 residues within 4Å: Chain A: N.227, D.229, S.230 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.227, A:D.229, A:D.229, A:S.230 SO4.5: 4 residues within 4Å: Chain A: K.309, T.310, A.311, S.312 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.309 SO4.6: 2 residues within 4Å: Chain A: K.520, S.616 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.616 Salt bridges: A:K.520

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 4 residues within 4Å: Chain A: P.568, V.569, R.570, H.626 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:V.569, A:R.570, A:R.570, A:H.626, A:H.626

1 x COA: COENZYME A(Non-covalent)

COA.8: 13 residues within 4Å: Chain A: P.40, V.41, A.43, A.79, A.81, D.82, I.83, L.118, P.142, L.146, Y.176, F.291, K.295 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:A.79, A:L.118, A:P.142 Hydrogen bonds: A:A.81, A:D.82, A:I.83, A:Y.176 Salt bridges: A:K.295, A:K.295

1 x NCA: NICOTINAMIDE(Non-covalent)

NCA.9: 12 residues within 4Å: Chain A: A.81, G.85, F.86, L.93, G.120, E.123, E.143, I.148, P.150, G.151, A.152, F.275 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.93, A:F.275, A:F.275 Hydrogen bonds: A:G.120, A:E.143, A:G.151, A:A.152

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sridhar, S. et al., Crystallographic binding studies of rat peroxisomal multifunctional enzyme type 1 with 3-ketodecanoyl-CoA: capturing active and inactive states of its hydratase and dehydrogenase catalytic sites. Acta Crystallogr D Struct Biol (2020)

Release Date

2020-12-09

Peptides

Peroxisomal bifunctional enzyme: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

Peroxisomal bifunctional enzyme

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