SMTL ID : 6hr8.1 (1 other biounit)

HMG-CoA reductase from Methanothermococcus thermolithotrophicus in complex with NADPH at 2.9 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-tetramer

Ligands

4 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.1: 15 residues within 4Å: Chain A: K.84, T.187, R.188, H.189, T.213, D.215, A.216, G.218, M.219, N.220, M.221, V.367, G.368, G.369, G.388 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:K.84 Hydrogen bonds: A:K.84, A:T.187, A:R.188, A:H.189, A:D.215, A:D.215, A:D.215, A:A.216, A:G.218, A:M.219, A:N.220, A:N.220, A:M.221, A:G.369 Salt bridges: A:H.189 pi-Stacking: A:H.189 pi-Cation interactions: A:H.189 NAP.6: 15 residues within 4Å: Chain B: T.186, T.187, R.188, H.189, T.213, D.215, A.216, M.217, G.218, M.219, N.220, M.221, V.367, G.368, G.369 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:T.187, B:R.188, B:H.189, B:D.215, B:D.215, B:A.216, B:M.217, B:G.218, B:M.219, B:N.220, B:N.220, B:M.221, B:G.369 Salt bridges: B:R.188 pi-Stacking: B:H.189, B:H.189 NAP.12: 15 residues within 4Å: Chain C: K.84, T.187, R.188, H.189, T.213, D.215, A.216, M.217, G.218, M.219, N.220, M.221, V.367, G.368, G.369 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:R.188, C:H.189, C:D.215, C:D.215, C:D.215, C:A.216, C:M.217, C:G.218, C:M.219, C:N.220, C:N.220, C:M.221, C:G.369 pi-Stacking: C:H.189, C:H.189 NAP.17: 13 residues within 4Å: Chain D: T.187, R.188, H.189, T.213, D.215, A.216, M.217, G.218, M.219, N.220, M.221, G.368, G.369 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:R.188, D:H.189, D:D.215, D:D.215, D:A.216, D:M.217, D:G.218, D:M.219, D:N.220, D:N.220, D:M.221, D:G.369 pi-Stacking: D:H.189, D:H.189

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

SO4.2: 4 residues within 4Å: Chain A: V.146, D.148, D.149, K.212 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.149 Salt bridges: A:K.212 SO4.7: 3 residues within 4Å: Chain B: N.111, E.113, F.114 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.113 Salt bridges: B:K.393 SO4.8: 4 residues within 4Å: Chain B: K.158, R.203 Chain D: T.349, E.350 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D Salt bridges: B:K.158, B:R.203 Hydrogen bonds: D:E.350 SO4.13: 4 residues within 4Å: Chain A: T.349, E.350 Chain C: K.158, R.203 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Salt bridges: C:K.158, C:R.203 Hydrogen bonds: A:E.350

10 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 6 residues within 4Å: Chain A: N.111, E.113, F.114, L.383, G.384 Chain B: S.64 No protein-ligand interaction detected (PLIP) PEG.4: 4 residues within 4Å: Chain A: C.139, F.277, K.279, E.282 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.279, A:E.282 PEG.5: 2 residues within 4Å: Chain A: I.193, D.194 No protein-ligand interaction detected (PLIP) PEG.9: 1 residues within 4Å: Chain B: D.194 No protein-ligand interaction detected (PLIP) PEG.10: 2 residues within 4Å: Chain B: V.146, K.212 No protein-ligand interaction detected (PLIP) PEG.11: 3 residues within 4Å: Chain B: K.50, G.72, Y.74 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.50, B:G.72, B:Y.74, B:E.78 PEG.14: 4 residues within 4Å: Chain C: E.113, F.114, G.384 Chain D: S.64 No protein-ligand interaction detected (PLIP) PEG.15: 4 residues within 4Å: Chain C: C.139, G.141, F.277, E.282 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.141, C:F.277 PEG.16: 3 residues within 4Å: Chain C: F.176, I.193, D.194 No protein-ligand interaction detected (PLIP) PEG.18: 4 residues within 4Å: Chain D: N.111, E.113, F.114, L.383 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.64

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

NA.19: 3 residues within 4Å: Chain D: C.139, K.279, E.282 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.282 NA.20: 1 residues within 4Å: Chain D: E.49 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.49

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
C

D
D

HMG-CoA reductase

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