SMTL ID : 5wpk.1

Structure of the class II 3-hydroxy-3-methylglutaryl-CoA reductase from Streptococcus pneumoniae bound to HMG-CoA and in a partially closed conformation

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x HMG: 3-HYDROXY-3-METHYLGLUTARYL-COENZYME A(Non-covalent)

HMG.1: 27 residues within 4Å: Chain A: W.7, N.8, G.9, F.10, S.11, E.83, S.85, V.86, A.88, A.89, S.91, Y.92, K.95, R.259, T.262, H.263, G.266, N.269, A.366, A.367, A.370, L.371, I.376, M.381 Chain B: E.52, N.53, I.211 19 PLIP interactions: 1 interactions with chain B, 18 interactions with chain A Water bridges: B:N.53, A:W.7, A:S.91, A:S.91, A:Y.92, A:Q.363, A:A.367 Hydrophobic interactions: A:A.89, A:Y.92, A:A.367 Hydrogen bonds: A:G.9, A:S.11, A:S.11, A:S.85, A:K.95, A:K.95, A:N.269 Salt bridges: A:K.95, A:R.259 HMG.4: 27 residues within 4Å: Chain A: E.52, N.53, I.211 Chain B: G.9, F.10, S.11, E.83, S.85, V.86, A.88, A.89, S.91, Y.92, R.259, T.262, H.263, G.266, N.269, A.366, A.367, A.370, L.371, I.376, G.379, K.382, L.383, K.386 20 PLIP interactions: 18 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:A.89, B:Y.92, B:L.383 Hydrogen bonds: B:G.9, B:F.10, B:S.11, B:S.11, B:S.11, B:K.386, A:N.53 Water bridges: B:S.91, B:N.269, B:N.269, B:Q.363, B:A.367, B:G.379, A:N.189 Salt bridges: B:R.259, B:K.382, B:K.386

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 8 residues within 4Å: Chain A: A.182, M.183, G.184, A.185, N.186, A.325, K.327, G.328 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:M.183, A:G.184, A:A.185, A:N.186, A:K.327 GOL.5: 5 residues within 4Å: Chain B: Q.106, H.108, T.222, E.317, T.319 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.106, B:T.222, B:T.319 GOL.6: 7 residues within 4Å: Chain B: L.141, A.142, A.145, Y.146, T.190, M.191, A.194 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.142, B:Q.144, B:A.145, B:M.191

2 x PE4: 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL(Non-functional Binders)

PE4.3: 6 residues within 4Å: Chain A: V.44, T.45, D.48 Chain B: S.14, Y.15, Q.16 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:D.48, B:S.14, B:Y.15, B:Q.16 PE4.7: 10 residues within 4Å: Chain B: I.5, W.7, Q.25, L.27, Q.73, E.74, Y.75, T.76, L.344, G.345 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:I.5, B:T.76, B:T.76 Water bridges: B:W.7

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Miller, B.R. et al., Structural Features and Domain Movements Controlling Substrate Binding and Cofactor Specificity in Class II HMG-CoA Reductase. Biochemistry (2018)

Release Date

2018-04-25

Peptides

3-hydroxy-3-methylglutaryl coenzyme A reductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

3-hydroxy-3-methylglutaryl coenzyme A reductase

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