SMTL ID : 8prw.1

Cryo-EM structure of the yeast fatty acid synthase at 1.9 angstrom resolution

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-6-mer

Ligands

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

NAP.1: 26 residues within 4Å: Chain A: G.682, G.684, S.687, I.688, T.707, S.708, R.709, F.737, N.738, Q.739, F.771, A.772, A.773, I.774, I.794, M.795, P.825, M.826, Y.839, K.843, I.869, G.870, T.872, T.875, G.876, L.877 30 PLIP interactions: 30 interactions with chain A Hydrophobic interactions: A:I.869, A:I.869 Hydrogen bonds: A:G.684, A:I.688, A:T.707, A:S.708, A:S.708, A:S.708, A:R.709, A:N.738, A:Q.739, A:G.740, A:F.771, A:A.773, A:K.843, A:T.872, A:T.872, A:T.872, A:T.875, A:G.876, A:L.877 Water bridges: A:G.682, A:G.682, A:A.683, A:K.685, A:G.689, A:R.709, A:R.709, A:A.773 Salt bridges: A:R.709 NAP.4: 18 residues within 4Å: Chain B: T.598, G.622, F.625, I.652, N.655, G.739, H.740, E.849, D.940, P.1010, Q.1012, K.1013, P.1014, K.1031, D.1032, L.1034, L.1054 Ligands: FNR.3 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:L.1034, B:L.1054 Hydrogen bonds: B:N.655, B:H.740, B:D.940, B:D.1032 Water bridges: B:D.1032, B:D.1032, B:S.1033, B:S.1033 Salt bridges: B:K.1031 pi-Stacking: B:F.625, B:F.625 pi-Cation interactions: B:H.740 NAP.5: 27 residues within 4Å: Chain C: G.682, G.684, S.687, I.688, T.707, S.708, R.709, F.737, N.738, Q.739, F.771, A.772, A.773, I.774, I.794, M.795, P.825, M.826, Y.839, K.843, I.869, G.870, T.872, T.875, G.876, L.877, M.878 30 PLIP interactions: 30 interactions with chain C Hydrophobic interactions: C:I.869, C:I.869 Hydrogen bonds: C:G.684, C:I.688, C:T.707, C:S.708, C:S.708, C:S.708, C:R.709, C:N.738, C:Q.739, C:G.740, C:F.771, C:A.773, C:K.843, C:T.872, C:T.872, C:T.872, C:T.875, C:G.876, C:L.877 Water bridges: C:G.682, C:G.682, C:A.683, C:K.685, C:G.689, C:R.709, C:R.709, C:A.773 Salt bridges: C:R.709 NAP.6: 27 residues within 4Å: Chain D: G.682, G.684, S.687, I.688, T.707, S.708, R.709, F.737, N.738, Q.739, F.771, A.772, A.773, I.774, I.794, M.795, P.825, M.826, Y.839, K.843, I.869, G.870, T.872, T.875, G.876, L.877, M.878 30 PLIP interactions: 30 interactions with chain D Hydrophobic interactions: D:I.869, D:I.869 Hydrogen bonds: D:G.684, D:I.688, D:T.707, D:S.708, D:S.708, D:S.708, D:R.709, D:N.738, D:Q.739, D:G.740, D:F.771, D:A.773, D:K.843, D:T.872, D:T.872, D:T.872, D:T.875, D:G.876, D:L.877 Water bridges: D:G.682, D:A.683, D:K.685, D:G.689, D:R.709, D:R.709, D:Y.718, D:A.773 Salt bridges: D:R.709 NAP.7: 27 residues within 4Å: Chain E: G.682, G.684, S.687, I.688, T.707, S.708, R.709, F.737, N.738, Q.739, F.771, A.772, A.773, I.774, I.794, M.795, P.825, M.826, Y.839, K.843, I.869, G.870, T.872, T.875, G.876, L.877, M.878 29 PLIP interactions: 29 interactions with chain E Hydrophobic interactions: E:I.869, E:I.869 Hydrogen bonds: E:G.684, E:I.688, E:S.708, E:S.708, E:S.708, E:R.709, E:N.738, E:Q.739, E:G.740, E:F.771, E:A.773, E:Y.839, E:K.843, E:T.872, E:T.872, E:T.875, E:G.876, E:L.877 Water bridges: E:G.682, E:G.682, E:A.683, E:K.685, E:G.689, E:R.709, E:R.709, E:A.773 Salt bridges: E:R.709 NAP.8: 26 residues within 4Å: Chain F: G.682, G.684, S.687, I.688, T.707, S.708, R.709, F.737, N.738, Q.739, F.771, A.772, A.773, I.774, I.794, M.795, P.825, M.826, Y.839, K.843, I.869, G.870, T.872, T.875, G.876, L.877 29 PLIP interactions: 29 interactions with chain F Hydrophobic interactions: F:I.869, F:I.869 Hydrogen bonds: F:G.684, F:I.688, F:S.708, F:S.708, F:S.708, F:R.709, F:N.738, F:Q.739, F:G.740, F:F.771, F:A.773, F:Y.839, F:K.843, F:T.872, F:T.872, F:T.875, F:G.876, F:L.877 Water bridges: F:G.682, F:G.682, F:A.683, F:K.685, F:G.689, F:R.709, F:R.709, F:A.773 Salt bridges: F:R.709 NAP.9: 27 residues within 4Å: Chain G: G.682, G.684, S.687, I.688, T.707, S.708, R.709, F.737, N.738, Q.739, F.771, A.772, A.773, I.774, I.794, M.795, P.825, M.826, Y.839, K.843, I.869, G.870, T.872, T.875, G.876, L.877, M.878 29 PLIP interactions: 29 interactions with chain G Hydrophobic interactions: G:I.869, G:I.869 Hydrogen bonds: G:G.684, G:I.688, G:S.708, G:S.708, G:S.708, G:R.709, G:N.738, G:Q.739, G:G.740, G:F.771, G:A.773, G:Y.839, G:K.843, G:T.872, G:T.872, G:T.875, G:G.876, G:L.877 Water bridges: G:G.682, G:G.682, G:A.683, G:K.685, G:G.689, G:R.709, G:R.709, G:A.773 Salt bridges: G:R.709 NAP.12: 18 residues within 4Å: Chain H: T.598, G.622, F.625, I.652, N.655, G.739, H.740, E.849, D.940, P.1010, Q.1012, K.1013, P.1014, K.1031, D.1032, L.1034, L.1054 Ligands: FNR.11 16 PLIP interactions: 16 interactions with chain H Hydrophobic interactions: H:L.1034, H:L.1054 Hydrogen bonds: H:T.598, H:N.655, H:H.740, H:H.740, H:D.940, H:D.1032 Water bridges: H:D.1032, H:D.1032, H:S.1033, H:S.1033 Salt bridges: H:K.1031 pi-Stacking: H:F.625, H:F.625 pi-Cation interactions: H:H.740 NAP.15: 18 residues within 4Å: Chain I: T.598, G.622, F.625, I.652, N.655, G.739, H.740, E.849, D.940, P.1010, Q.1012, K.1013, P.1014, K.1031, D.1032, L.1034, L.1054 Ligands: FNR.14 14 PLIP interactions: 14 interactions with chain I Hydrophobic interactions: I:L.1034, I:L.1054 Hydrogen bonds: I:N.655, I:H.740, I:D.940, I:D.1032 Water bridges: I:D.1032, I:D.1032, I:S.1033, I:S.1033 Salt bridges: I:K.1031 pi-Stacking: I:F.625, I:F.625 pi-Cation interactions: I:H.740 NAP.18: 18 residues within 4Å: Chain J: T.598, G.622, F.625, I.652, N.655, G.739, H.740, E.849, D.940, P.1010, Q.1012, K.1013, P.1014, K.1031, D.1032, L.1034, L.1054 Ligands: FNR.17 14 PLIP interactions: 14 interactions with chain J Hydrophobic interactions: J:L.1034, J:L.1054 Hydrogen bonds: J:N.655, J:H.740, J:D.940, J:D.1032 Water bridges: J:D.1032, J:D.1032, J:S.1033, J:S.1033 Salt bridges: J:K.1031 pi-Stacking: J:F.625, J:F.625 pi-Cation interactions: J:H.740 NAP.21: 18 residues within 4Å: Chain K: T.598, G.622, F.625, I.652, N.655, G.739, H.740, E.849, D.940, P.1010, Q.1012, K.1013, P.1014, K.1031, D.1032, L.1034, L.1054 Ligands: FNR.20 16 PLIP interactions: 16 interactions with chain K Hydrophobic interactions: K:L.1034, K:L.1054 Hydrogen bonds: K:T.598, K:N.655, K:H.740, K:H.740, K:D.940, K:D.1032 Water bridges: K:D.1032, K:D.1032, K:S.1033, K:S.1033 Salt bridges: K:K.1031 pi-Stacking: K:F.625, K:F.625 pi-Cation interactions: K:H.740 NAP.24: 18 residues within 4Å: Chain L: T.598, G.622, F.625, I.652, N.655, G.739, H.740, E.849, D.940, P.1010, Q.1012, K.1013, P.1014, K.1031, D.1032, L.1034, L.1054 Ligands: FNR.23 16 PLIP interactions: 16 interactions with chain L Hydrophobic interactions: L:L.1034, L:L.1054 Hydrogen bonds: L:T.598, L:N.655, L:H.740, L:H.740, L:D.940, L:D.1032 Water bridges: L:D.1032, L:D.1032, L:S.1033, L:S.1033 Salt bridges: L:K.1031 pi-Stacking: L:F.625, L:F.625 pi-Cation interactions: L:H.740

6 x COA: COENZYME A(Non-covalent)

COA.2: 21 residues within 4Å: Chain A: M.56, R.59 Chain B: Q.1669, H.1807, S.1808, M.1854, A.1856, I.1857, N.1858, R.1861, N.1890, N.1892, Q.1897, V.1899, R.1962, F.1964, A.1965, C.1966, I.1967, F.1976, H.1977 14 PLIP interactions: 13 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:A.1856 Hydrogen bonds: B:Q.1669, B:N.1858, B:R.1861, B:R.1861, B:N.1892, B:Q.1897, B:Q.1897, B:R.1962, B:R.1962, B:A.1965 Salt bridges: B:R.1861, A:R.59 pi-Cation interactions: B:R.1861 COA.10: 21 residues within 4Å: Chain G: M.56, R.59 Chain H: Q.1669, H.1807, S.1808, M.1854, A.1856, N.1858, R.1861, N.1890, N.1892, Q.1897, V.1899, R.1962, G.1963, F.1964, A.1965, C.1966, I.1967, F.1976, H.1977 14 PLIP interactions: 13 interactions with chain H, 1 interactions with chain G Hydrophobic interactions: H:A.1856 Hydrogen bonds: H:Q.1669, H:N.1858, H:R.1861, H:N.1892, H:Q.1897, H:Q.1897, H:R.1962, H:R.1962, H:A.1965 Salt bridges: H:R.1861, G:R.59 pi-Cation interactions: H:R.1861, H:R.1861 COA.13: 21 residues within 4Å: Chain C: M.56, R.59 Chain I: Q.1669, H.1807, S.1808, M.1854, A.1856, N.1858, R.1861, N.1890, N.1892, Q.1897, V.1899, R.1962, G.1963, F.1964, A.1965, C.1966, I.1967, F.1976, H.1977 14 PLIP interactions: 13 interactions with chain I, 1 interactions with chain C Hydrophobic interactions: I:A.1856 Hydrogen bonds: I:Q.1669, I:N.1858, I:R.1861, I:N.1892, I:Q.1897, I:Q.1897, I:R.1962, I:R.1962, I:A.1965 Salt bridges: I:R.1861, C:R.59 pi-Cation interactions: I:R.1861, I:R.1861 COA.16: 22 residues within 4Å: Chain D: M.56, R.59 Chain J: Q.1669, H.1807, S.1808, M.1854, A.1856, N.1858, R.1861, N.1890, N.1892, Q.1897, V.1899, R.1962, G.1963, F.1964, A.1965, C.1966, I.1967, L.1969, F.1976, H.1977 14 PLIP interactions: 13 interactions with chain J, 1 interactions with chain D Hydrophobic interactions: J:A.1856 Hydrogen bonds: J:Q.1669, J:N.1858, J:R.1861, J:N.1892, J:Q.1897, J:Q.1897, J:R.1962, J:R.1962, J:A.1965 Salt bridges: J:R.1861, D:R.59 pi-Cation interactions: J:R.1861, J:R.1861 COA.19: 22 residues within 4Å: Chain E: M.56, R.59 Chain K: Q.1669, H.1807, S.1808, M.1854, A.1856, N.1858, R.1861, N.1890, N.1892, Q.1897, V.1899, R.1962, G.1963, F.1964, A.1965, C.1966, I.1967, L.1969, F.1976, H.1977 14 PLIP interactions: 1 interactions with chain E, 13 interactions with chain K Salt bridges: E:R.59, K:R.1861 Hydrophobic interactions: K:A.1856 Hydrogen bonds: K:Q.1669, K:N.1858, K:R.1861, K:N.1892, K:Q.1897, K:Q.1897, K:R.1962, K:R.1962, K:A.1965 pi-Cation interactions: K:R.1861, K:R.1861 COA.22: 21 residues within 4Å: Chain F: M.56, R.59 Chain L: Q.1669, H.1807, S.1808, M.1854, A.1856, I.1857, N.1858, R.1861, N.1890, N.1892, Q.1897, V.1899, R.1962, F.1964, A.1965, C.1966, I.1967, F.1976, H.1977 14 PLIP interactions: 13 interactions with chain L, 1 interactions with chain F Hydrophobic interactions: L:A.1856 Hydrogen bonds: L:Q.1669, L:N.1858, L:R.1861, L:R.1861, L:N.1892, L:Q.1897, L:Q.1897, L:R.1962, L:R.1962, L:A.1965 Salt bridges: L:R.1861, F:R.59 pi-Cation interactions: L:R.1861

6 x FNR: 1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL(Non-covalent)

FNR.3: 21 residues within 4Å: Chain B: P.595, G.596, M.597, T.598, C.600, N.650, I.652, G.682, K.706, T.733, G.737, G.738, S.769, G.770, L.800, G.802, S.803, M.806, L.1054, A.1059 Ligands: NAP.4 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:M.597, B:L.1054, B:L.1054 Hydrogen bonds: B:G.596, B:T.598, B:T.598, B:T.598, B:N.650, B:N.650, B:K.706, B:K.706, B:K.706, B:G.738, B:G.738, B:S.769, B:G.770, B:G.802, B:S.803 Water bridges: B:F.771, B:F.771, B:A.1059 FNR.11: 21 residues within 4Å: Chain H: P.595, G.596, M.597, T.598, C.600, N.650, I.652, G.682, K.706, T.733, G.737, G.738, S.769, G.770, L.800, G.802, S.803, M.806, L.1054, A.1059 Ligands: NAP.12 19 PLIP interactions: 19 interactions with chain H Hydrophobic interactions: H:M.597, H:L.1054, H:L.1054 Hydrogen bonds: H:G.596, H:T.598, H:T.598, H:N.650, H:N.650, H:K.706, H:K.706, H:K.706, H:G.738, H:G.738, H:S.769, H:G.770, H:G.802, H:S.803 Water bridges: H:F.771, H:F.771 FNR.14: 21 residues within 4Å: Chain I: P.595, G.596, M.597, T.598, C.600, N.650, I.652, G.682, K.706, T.733, G.737, G.738, S.769, G.770, L.800, G.802, S.803, M.806, L.1054, A.1059 Ligands: NAP.15 20 PLIP interactions: 20 interactions with chain I Hydrophobic interactions: I:M.597, I:L.1054, I:L.1054 Hydrogen bonds: I:G.596, I:T.598, I:T.598, I:T.598, I:N.650, I:N.650, I:K.706, I:K.706, I:K.706, I:G.738, I:G.738, I:S.769, I:G.770, I:G.802, I:S.803 Water bridges: I:F.771, I:F.771 FNR.17: 21 residues within 4Å: Chain J: P.595, G.596, M.597, T.598, C.600, N.650, I.652, G.682, K.706, T.733, G.737, G.738, S.769, G.770, L.800, G.802, S.803, M.806, L.1054, A.1059 Ligands: NAP.18 21 PLIP interactions: 21 interactions with chain J Hydrophobic interactions: J:M.597, J:L.1054, J:L.1054 Hydrogen bonds: J:G.596, J:T.598, J:T.598, J:T.598, J:N.650, J:N.650, J:K.706, J:K.706, J:K.706, J:G.738, J:G.738, J:S.769, J:G.770, J:G.802, J:S.803 Water bridges: J:F.771, J:F.771, J:A.1059 FNR.20: 21 residues within 4Å: Chain K: P.595, G.596, M.597, T.598, C.600, N.650, I.652, G.682, K.706, T.733, G.737, G.738, S.769, G.770, L.800, G.802, S.803, M.806, L.1054, A.1059 Ligands: NAP.21 20 PLIP interactions: 20 interactions with chain K Hydrophobic interactions: K:M.597, K:L.1054, K:L.1054 Hydrogen bonds: K:G.596, K:T.598, K:T.598, K:N.650, K:N.650, K:K.706, K:K.706, K:K.706, K:G.738, K:G.738, K:S.769, K:G.770, K:G.802, K:S.803 Water bridges: K:F.771, K:F.771, K:A.1059 FNR.23: 21 residues within 4Å: Chain L: P.595, G.596, M.597, T.598, C.600, N.650, I.652, G.682, K.706, T.733, G.737, G.738, S.769, G.770, L.800, G.802, S.803, M.806, L.1054, A.1059 Ligands: NAP.24 20 PLIP interactions: 20 interactions with chain L Hydrophobic interactions: L:M.597, L:L.1054, L:L.1054 Hydrogen bonds: L:G.596, L:T.598, L:T.598, L:N.650, L:N.650, L:K.706, L:K.706, L:K.706, L:G.738, L:G.738, L:S.769, L:G.770, L:G.802, L:S.803 Water bridges: L:F.771, L:F.771, L:A.1059

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singh, K. et al., Reconstruction of a fatty acid synthesis cycle from acyl carrier protein and cofactor structural snapshots. Cell (2023)

Release Date

2023-11-22

Peptides

Fatty acid synthase subunit alpha: ACDEFG
Fatty acid synthase subunit beta: BHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
B

D
C

E
D

F
E

G
F

B
G

H
J

I
I

J
H

K
K

L
L

Fatty acid synthase subunit alpha

Fatty acid synthase subunit beta

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