SMTL ID : 6hr7.1

HMG-CoA reductase from Methanothermococcus thermolithotrophicus apo form at 2.4 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

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

SO4.1: 6 residues within 4Å: Chain A: A.216, M.217, G.218, M.219, N.220, M.221 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:M.217, A:G.218, A:M.219, A:N.220, A:N.220, A:M.221 SO4.2: 2 residues within 4Å: Chain A: R.188, H.189 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.188, A:H.189 SO4.10: 6 residues within 4Å: Chain B: A.216, M.217, G.218, M.219, N.220, M.221 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.218, B:M.219, B:N.220, B:M.221 SO4.11: 3 residues within 4Å: Chain B: R.145 Chain C: I.163, K.167 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Salt bridges: B:R.145, C:K.167 SO4.14: 6 residues within 4Å: Chain C: A.216, M.217, G.218, M.219, N.220, M.221 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:M.217, C:G.218, C:M.219, C:N.220, C:N.220, C:M.221 SO4.15: 2 residues within 4Å: Chain C: R.188, H.189 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:R.188, C:H.189 SO4.23: 6 residues within 4Å: Chain D: A.216, M.217, G.218, M.219, N.220, M.221 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:G.218, D:M.219, D:N.220, D:M.221 SO4.24: 3 residues within 4Å: Chain A: I.163, K.167 Chain D: R.145 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A Salt bridges: D:R.145, A:K.167

4 x DTT: 2,3-DIHYDROXY-1,4-DITHIOBUTANE(Non-covalent)

DTT.3: 7 residues within 4Å: Chain A: N.111, F.114, E.381, L.382, G.384, K.393 Chain B: S.64 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.382, A:K.393, A:K.393 DTT.4: 2 residues within 4Å: Chain A: I.29, I.38 No protein-ligand interaction detected (PLIP) DTT.16: 7 residues within 4Å: Chain C: N.111, F.114, E.381, L.382, G.384, K.393 Chain D: S.64 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:L.382, C:K.393, C:K.393 DTT.17: 2 residues within 4Å: Chain C: I.29, I.38 No protein-ligand interaction detected (PLIP)

2 x NA: SODIUM ION(Non-functional Binders)

NA.5: 2 residues within 4Å: Chain A: E.80, R.372 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.372 NA.18: 2 residues within 4Å: Chain C: E.80, R.372 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.80

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 3 residues within 4Å: Chain A: K.173, F.176, D.194 No protein-ligand interaction detected (PLIP) GOL.7: 4 residues within 4Å: Chain A: D.45, L.46, V.47, G.48 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.45 GOL.8: 4 residues within 4Å: Chain A: T.349, E.350 Chain D: K.158, R.203 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:K.158, D:R.203, D:R.203 GOL.12: 4 residues within 4Å: Chain B: K.173, F.176, I.193, D.194 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.173, B:I.193 GOL.19: 3 residues within 4Å: Chain C: K.173, F.176, D.194 No protein-ligand interaction detected (PLIP) GOL.20: 4 residues within 4Å: Chain C: D.45, L.46, V.47, G.48 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.45 GOL.21: 4 residues within 4Å: Chain B: K.158, R.203 Chain C: T.349, E.350 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.158, B:R.203, B:R.203 GOL.25: 4 residues within 4Å: Chain D: K.173, F.176, I.193, D.194 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.173, D:I.193

2 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)

P6G.9: 2 residues within 4Å: Chain A: E.31, K.35 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.31 P6G.22: 2 residues within 4Å: Chain C: E.31, K.35 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.31, C:E.31

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

CL.13: 2 residues within 4Å: Chain B: K.167 Chain C: R.145 Ligand excluded by PLIP CL.26: 2 residues within 4Å: Chain A: R.145 Chain D: K.167 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vogeli, B. et al., Crystal structure of archaeal HMG-CoA reductase: insights into structural changes of the C-terminal helix of the class-I enzyme. Febs Lett. (2019)

Release Date

2019-02-13

Peptides

HMG-CoA reductase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

HMG-CoA reductase

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