SMTL ID : 8ciw.1

Methylsuccinyl-CoA dehydrogenase from Pseudomonas migulae with bound FAD and (2S)-methylsuccinyl-CoA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

homo-dimer

Ligands

2 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.1: 31 residues within 4Å: Chain A: Q.47, R.242, I.275, I.277, T.278, G.283, S.284, W.308, T.310, Y.370, S.375, V.526, I.529, F.530, E.531, A.533, E.535, T.536, L.539, K.540 Chain B: R.437, V.439, F.440, L.444, Y.447, Q.504, I.505, G.507, G.508, Y.511 Ligands: ZKK.2 34 PLIP interactions: 26 interactions with chain A, 8 interactions with chain B Hydrophobic interactions: A:W.308, A:W.308, A:Y.370, A:F.530, B:Y.511 Hydrogen bonds: A:Q.47, A:R.242, A:I.275, A:I.277, A:T.278, A:T.278, A:S.284, A:S.284, A:T.310, A:E.531, A:E.535, A:E.535, A:T.536, A:T.536, B:Q.504, B:G.508 Water bridges: A:T.278, A:G.283, A:G.283, A:D.285, A:G.532, A:K.540, A:K.540, B:R.437, B:R.437, B:M.509 pi-Stacking: A:F.530 Salt bridges: B:R.437, B:R.437 FAD.6: 33 residues within 4Å: Chain A: R.437, V.439, F.440, L.444, Y.447, Q.504, I.505, G.507, G.508, Y.511 Chain B: Q.47, R.242, I.275, A.276, I.277, T.278, G.283, S.284, W.308, C.309, T.310, Y.370, S.375, V.526, I.529, F.530, E.531, A.533, E.535, T.536, L.539, K.540 Ligands: ZKK.7 37 PLIP interactions: 10 interactions with chain A, 27 interactions with chain B Hydrophobic interactions: A:Y.511, A:Y.511, B:W.308, B:W.308, B:Y.370, B:V.526, B:F.530 Hydrogen bonds: A:Q.504, A:G.508, B:Q.47, B:R.242, B:I.275, B:I.277, B:T.278, B:T.278, B:S.284, B:S.284, B:T.310, B:T.310, B:E.531, B:E.535, B:E.535, B:T.536, B:T.536, B:K.540 Water bridges: A:R.437, A:Y.447, A:Y.447, A:M.509, B:I.275, B:T.278, B:G.283, B:G.283, B:D.285, B:A.533 Salt bridges: A:R.437, A:R.437

2 x ZKK: (2S)-Methylsuccinyl-CoA(Non-covalent)

ZKK.2: 26 residues within 4Å: Chain A: T.241, R.242, I.245, G.283, S.284, V.286, A.287, T.310, H.332, Y.370, F.401, Y.402, M.405, M.408, R.412, R.418, R.481, F.530, E.531, G.532, T.536, K.540, V.541, R.544 Chain B: F.440 Ligands: FAD.1 29 PLIP interactions: 28 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.245, A:V.286, A:F.530, A:E.531, A:T.536, A:K.540, A:V.541, B:F.440 Hydrogen bonds: A:S.284, A:V.286, A:T.310, A:T.310, A:Y.402, A:T.409, A:T.409, A:R.412, A:E.531 Water bridges: A:D.285, A:A.287, A:R.412, A:R.481, A:R.481, A:R.544, A:R.544 Salt bridges: A:R.242, A:H.332, A:R.418, A:R.544, A:R.544 ZKK.7: 26 residues within 4Å: Chain A: F.440 Chain B: T.241, R.242, T.278, G.283, S.284, V.286, T.310, H.332, R.333, Y.370, F.401, Y.402, M.405, M.408, T.409, R.412, R.418, R.481, F.530, E.531, G.532, T.536, V.541, R.544 Ligands: FAD.6 31 PLIP interactions: 30 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:V.286, B:F.530, B:E.531, B:T.536, B:V.541, A:F.440 Hydrogen bonds: B:S.284, B:V.286, B:T.310, B:Y.370, B:Y.402, B:T.409, B:T.409, B:R.412, B:E.531, B:E.531 Water bridges: B:D.285, B:D.285, B:A.287, B:R.412, B:R.481, B:R.481, B:R.544, B:R.544, B:R.544 Salt bridges: B:R.242, B:H.332, B:R.333, B:R.418, B:R.544, B:R.544

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

P6G.3: 5 residues within 4Å: Chain A: L.449, A.452, K.453, K.456 Chain B: V.48 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.456 P6G.5: 8 residues within 4Å: Chain A: V.48 Chain B: E.88, L.133, L.449, A.452, K.453, K.456, E.501 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.456

1 x FLC: CITRATE ANION(Non-covalent)

FLC.4: 3 residues within 4Å: Chain B: G.347, H.348, E.349 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:E.349 Hydrogen bonds: B:H.348, B:E.349, B:E.349, B:E.349 Water bridges: B:G.347 Salt bridges: B:H.348

1 x COA: COENZYME A(Non-covalent)

COA.8: 4 residues within 4Å: Chain B: W.300, T.324, P.326, L.397 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.324

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

McLean, R. et al., Exploring alternative pathways for the in vitro establishment of the HOPAC cycle for synthetic CO 2 fixation. Sci Adv (2023)

Release Date

2023-07-12

Peptides

(2S)-methylsuccinyl-CoA dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

(2S)-methylsuccinyl-CoA dehydrogenase