SMTL ID : 6z5v.1 (1 other biounit)

CRYSTAL STRUCTURE OF RAT PEROXISOMAL MULTIFUNCTIONAL ENZYME TYPE-1 (RPMFE1) COMPLEXED WITH 3-KETODECANOYL-COA IN CROTONASE FOLD AND OXIDISED NICOTINAMIDE ADENINE DINUCLEOTIDE IN HAD FOLD

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.33 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 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:L.324, A:T.326, A:T.326, A:T.326, A:T.326, A:M.327, A:S.347, A:K.408, A:K.408, A:N.428, A:S.430, A:S.454 pi-Stacking: A:F.402

1 x ZOZ: 3-KETO-DECANOYL-COA(Non-covalent)

ZOZ.2: 28 residues within 4Å: Chain A: P.40, V.41, V.44, S.45, P.46, I.49, A.79, G.80, A.81, D.82, I.83, H.84, F.86, P.91, G.92, L.95, V.116, L.118, G.119, G.120, E.123, R.138, P.142, E.143, L.146, Y.176, F.275, K.295 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:I.49, A:A.79, A:F.86, A:P.91, A:L.95, A:V.116, A:V.116, A:E.143, A:F.275 Hydrogen bonds: A:A.79, A:A.81, A:A.81, A:I.83, A:G.120, A:Y.176 Salt bridges: A:K.295

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: N.509, F.512, R.553, Y.577, S.578 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.509, A:R.553, A:S.578, A:S.578

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

SO4.4: 4 residues within 4Å: Chain A: P.211, I.212, E.213, R.216 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.212, A:E.213 Salt bridges: A:R.216 SO4.5: 2 residues within 4Å: Chain A: S.296, R.661 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.661

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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