SMTL ID : 6fah.1

Molecular basis of the flavin-based electron-bifurcating caffeyl-CoA reductase reaction

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.13 Å

Oligo State

hetero-4-4-4-mer

Ligands

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

FAD.1: 29 residues within 4Å: Chain A: G.283, M.284, G.285, S.309, R.310, A.311, V.324, G.325, Q.326, T.327, G.328, G.340, I.341, S.342, G.343, A.344, Q.346, H.347, N.361, K.362, N.363, G.378, D.379, L.380 Chain C: Y.340, Y.346 Chain D: P.127, R.152, E.198 22 PLIP interactions: 5 interactions with chain D, 14 interactions with chain A, 3 interactions with chain C Hydrogen bonds: D:R.152, D:D.210, D:D.210, A:M.284, A:S.309, A:S.309, A:R.310, A:V.324, A:T.327, A:G.328, A:S.342, A:G.343, A:Q.346, A:N.361, A:K.362, A:D.379, A:L.380 Salt bridges: D:R.152, D:R.152 Hydrophobic interactions: C:Y.340, C:Y.340, C:Y.346 FAD.4: 32 residues within 4Å: Chain A: L.183, T.184, R.203, A.205, F.206, A.212, I.214 Chain B: C.6, A.7, K.8, N.35, D.38, M.60, T.61, M.62, A.93, D.94, T.95, T.98, L.102, A.117, G.118, Q.120, A.121, G.124, D.125, T.126, A.127, Q.128, V.129, T.223, V.225 24 PLIP interactions: 19 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:K.8, B:N.35, B:D.38, B:M.62, B:M.62, B:D.94, B:D.94, B:T.95, B:T.98, B:G.118, B:G.118, B:A.121, B:T.126, B:T.126, B:A.127, B:Q.128, B:V.129, B:T.223, A:L.183, A:R.203, A:R.203 Salt bridges: B:K.8 Hydrophobic interactions: A:A.205, A:A.212 FAD.5: 27 residues within 4Å: Chain C: F.122, L.124, T.125, G.130, S.131, F.155, T.157, K.200, V.357, Y.361, E.362, G.363, T.364, Q.366, M.370 Chain D: R.267, Q.269, F.270, I.274, F.277, I.280, Q.335, I.336, G.338, G.339, Y.340 Chain I: Q.278 22 PLIP interactions: 15 interactions with chain C, 6 interactions with chain D, 1 interactions with chain I Hydrophobic interactions: C:F.155, C:V.357, C:Y.361 Hydrogen bonds: C:F.122, C:L.124, C:T.125, C:T.125, C:S.131, C:S.131, C:T.157, C:T.157, C:E.362, C:G.363, C:T.364, C:T.364, D:R.267, D:Q.269, D:I.336, D:G.339, I:Q.278 Salt bridges: D:R.267 pi-Stacking: D:F.277 FAD.11: 25 residues within 4Å: Chain C: Y.263, R.267, Q.269, F.270, I.274, F.277, I.280, Q.335, I.336, G.338, G.339 Chain D: F.122, L.124, T.125, G.130, S.131, F.155, T.157, V.357, Y.361, E.362, T.364, Q.366, M.370 Chain J: Q.278 17 PLIP interactions: 10 interactions with chain D, 6 interactions with chain C, 1 interactions with chain J Hydrophobic interactions: D:F.155, D:V.357 Hydrogen bonds: D:F.122, D:L.124, D:T.125, D:T.125, D:S.131, D:T.157, D:E.362, D:T.364, C:Y.263, C:R.267, C:Q.335, C:I.336, C:G.339, J:Q.278 Salt bridges: C:R.267 FAD.14: 30 residues within 4Å: Chain C: R.152, E.198, D.210 Chain D: Y.346 Chain E: G.283, M.284, G.285, S.309, R.310, A.311, Q.323, V.324, G.325, Q.326, T.327, G.328, G.340, I.341, S.342, G.343, A.344, Q.346, H.347, I.360, N.361, K.362, N.363, G.378, D.379, L.380 22 PLIP interactions: 1 interactions with chain D, 18 interactions with chain E, 3 interactions with chain C Hydrophobic interactions: D:Y.346 Hydrogen bonds: E:M.284, E:S.309, E:S.309, E:R.310, E:Q.323, E:V.324, E:T.327, E:G.328, E:S.342, E:S.342, E:G.343, E:H.347, E:N.361, E:K.362, E:N.363, E:D.379, E:D.379, E:L.380, C:D.210 Salt bridges: C:R.152, C:R.152 FAD.17: 28 residues within 4Å: Chain E: L.183, R.203, I.214 Chain F: C.6, A.7, K.8, N.35, D.38, M.60, T.61, M.62, A.93, D.94, T.95, T.98, L.102, A.117, G.118, Q.120, A.121, G.124, D.125, T.126, A.127, Q.128, V.129, T.223, V.225 21 PLIP interactions: 18 interactions with chain F, 3 interactions with chain E Hydrophobic interactions: F:V.225 Hydrogen bonds: F:N.35, F:D.38, F:T.61, F:M.62, F:M.62, F:D.94, F:T.95, F:G.118, F:G.118, F:A.121, F:T.126, F:T.126, F:A.127, F:Q.128, F:V.129, F:T.223, E:L.183, E:R.203, E:R.203 Salt bridges: F:K.8 FAD.18: 29 residues within 4Å: Chain G: G.283, M.284, G.285, S.309, R.310, A.311, V.324, G.325, Q.326, T.327, G.328, G.340, I.341, S.342, G.343, A.344, Q.346, H.347, N.361, K.362, N.363, G.378, D.379, L.380 Chain I: Y.340, Y.346 Chain J: P.127, R.152, E.198 23 PLIP interactions: 16 interactions with chain G, 4 interactions with chain J, 3 interactions with chain I Hydrogen bonds: G:M.284, G:S.309, G:S.309, G:R.310, G:V.324, G:T.327, G:G.328, G:S.342, G:G.343, G:Q.346, G:H.347, G:N.361, G:K.362, G:D.379, G:D.379, G:L.380, J:R.152, J:D.210 Salt bridges: J:R.152, J:R.152 Hydrophobic interactions: I:Y.340, I:Y.340, I:Y.346 FAD.21: 32 residues within 4Å: Chain G: L.183, T.184, R.203, A.205, F.206, A.212, I.214 Chain H: C.6, A.7, K.8, N.35, D.38, M.60, T.61, M.62, A.93, D.94, T.95, T.98, L.102, A.117, G.118, Q.120, A.121, G.124, D.125, T.126, A.127, Q.128, V.129, T.223, V.225 23 PLIP interactions: 5 interactions with chain G, 18 interactions with chain H Hydrophobic interactions: G:A.205, G:A.212 Hydrogen bonds: G:L.183, G:R.203, G:R.203, H:K.8, H:N.35, H:D.38, H:T.61, H:M.62, H:M.62, H:D.94, H:T.95, H:G.118, H:G.118, H:A.121, H:T.126, H:T.126, H:A.127, H:Q.128, H:V.129, H:T.223 Salt bridges: H:K.8 FAD.22: 27 residues within 4Å: Chain C: Q.278 Chain I: F.122, L.124, T.125, G.130, S.131, F.155, T.157, K.200, V.357, Y.361, E.362, G.363, T.364, Q.366, M.370 Chain J: R.267, Q.269, F.270, I.274, F.277, I.280, Q.335, I.336, G.338, G.339, Y.340 20 PLIP interactions: 13 interactions with chain I, 6 interactions with chain J, 1 interactions with chain C Hydrophobic interactions: I:F.155, I:V.357, I:Y.361 Hydrogen bonds: I:F.122, I:L.124, I:T.125, I:T.125, I:S.131, I:S.131, I:T.157, I:E.362, I:G.363, I:T.364, J:R.267, J:Q.269, J:I.336, J:G.339, C:Q.278 Salt bridges: J:R.267 pi-Stacking: J:F.277 FAD.28: 25 residues within 4Å: Chain D: Q.278 Chain I: Y.263, R.267, Q.269, F.270, I.274, F.277, I.280, Q.335, I.336, G.338, G.339 Chain J: F.122, L.124, T.125, G.130, S.131, F.155, T.157, V.357, Y.361, E.362, T.364, Q.366, M.370 18 PLIP interactions: 5 interactions with chain I, 1 interactions with chain D, 12 interactions with chain J Hydrogen bonds: I:R.267, I:Q.335, I:I.336, I:G.339, D:Q.278, J:F.122, J:L.124, J:T.125, J:T.125, J:S.131, J:T.157, J:T.157, J:E.362, J:T.364, J:T.364 Salt bridges: I:R.267 Hydrophobic interactions: J:F.155, J:V.357 FAD.31: 30 residues within 4Å: Chain I: R.152, E.198, D.210 Chain J: Y.346 Chain K: G.283, M.284, G.285, S.309, R.310, A.311, Q.323, V.324, G.325, Q.326, T.327, G.328, G.340, I.341, S.342, G.343, A.344, Q.346, H.347, I.360, N.361, K.362, N.363, G.378, D.379, L.380 22 PLIP interactions: 16 interactions with chain K, 1 interactions with chain J, 5 interactions with chain I Hydrogen bonds: K:M.284, K:S.309, K:S.309, K:R.310, K:Q.323, K:V.324, K:T.327, K:G.328, K:S.342, K:S.342, K:G.343, K:N.361, K:K.362, K:N.363, K:D.379, K:L.380, I:R.152, I:D.210, I:D.210 Hydrophobic interactions: J:Y.346 Salt bridges: I:R.152, I:R.152 FAD.34: 28 residues within 4Å: Chain K: L.183, R.203, I.214 Chain L: C.6, A.7, K.8, N.35, D.38, M.60, T.61, M.62, A.93, D.94, T.95, T.98, L.102, A.117, G.118, Q.120, A.121, G.124, D.125, T.126, A.127, Q.128, V.129, T.223, V.225 21 PLIP interactions: 18 interactions with chain L, 3 interactions with chain K Hydrophobic interactions: L:V.225 Hydrogen bonds: L:N.35, L:D.38, L:M.62, L:M.62, L:D.94, L:D.94, L:T.95, L:T.98, L:G.118, L:G.118, L:A.121, L:T.126, L:T.126, L:A.127, L:Q.128, L:V.129, K:L.183, K:R.203, K:R.203 Salt bridges: L:K.8

8 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.2: 7 residues within 4Å: Chain A: C.10, G.12, C.13, S.14, C.16, C.48, A.52 5 PLIP interactions: 5 interactions with chain A, Metal complexes: A:C.10, A:C.13, A:C.16, A:C.16, A:C.48 SF4.3: 8 residues within 4Å: Chain A: C.20, P.21, A.37, C.38, T.39, N.40, C.41, C.44 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.20, A:C.38, A:C.41, A:C.44 SF4.15: 7 residues within 4Å: Chain E: C.10, I.11, C.13, C.16, C.48, A.52, I.53 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.10, E:C.13, E:C.16, E:C.48 SF4.16: 7 residues within 4Å: Chain E: C.20, P.21, C.38, T.39, N.40, C.41, C.44 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.20, E:C.38, E:C.41, E:C.44 SF4.19: 7 residues within 4Å: Chain G: C.10, G.12, C.13, S.14, C.16, C.48, A.52 5 PLIP interactions: 5 interactions with chain G, Metal complexes: G:C.10, G:C.13, G:C.16, G:C.16, G:C.48 SF4.20: 8 residues within 4Å: Chain G: C.20, P.21, A.37, C.38, T.39, N.40, C.41, C.44 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.20, G:C.38, G:C.41, G:C.44 SF4.32: 7 residues within 4Å: Chain K: C.10, I.11, C.13, C.16, C.48, A.52, I.53 4 PLIP interactions: 4 interactions with chain K, Metal complexes: K:C.10, K:C.13, K:C.16, K:C.48 SF4.33: 7 residues within 4Å: Chain K: C.20, P.21, C.38, T.39, N.40, C.41, C.44 4 PLIP interactions: 4 interactions with chain K, Metal complexes: K:C.20, K:C.38, K:C.41, K:C.44

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

SO4.6: 2 residues within 4Å: Chain C: K.344 Chain D: K.344 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Salt bridges: D:K.344, D:R.353, C:K.344, C:R.353 SO4.7: 4 residues within 4Å: Chain C: E.324, R.356 Chain D: K.332, Q.335 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.324 Salt bridges: C:R.356 SO4.8: 3 residues within 4Å: Chain C: D.286, K.290 Chain I: Y.321 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:K.290 SO4.9: 5 residues within 4Å: Chain A: Q.326 Chain C: E.259, E.345, Y.346, K.347 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.345, C:K.347 Salt bridges: C:K.262 SO4.10: 5 residues within 4Å: Chain C: S.87, T.157, Q.248, Y.361, E.362 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.87, C:Y.361, C:Y.361 SO4.12: 3 residues within 4Å: Chain D: V.84, Y.361, E.362 No protein-ligand interaction detected (PLIP) SO4.13: 5 residues within 4Å: Chain D: E.19, L.22, T.24, V.78, K.347 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.24 Salt bridges: D:K.347 SO4.23: 2 residues within 4Å: Chain I: K.344 Chain J: K.344 4 PLIP interactions: 2 interactions with chain I, 2 interactions with chain J Salt bridges: I:K.344, I:R.353, J:K.344, J:R.353 SO4.24: 4 residues within 4Å: Chain I: E.324, R.356 Chain J: K.332, Q.335 3 PLIP interactions: 3 interactions with chain I Hydrogen bonds: I:E.324, I:T.359 Salt bridges: I:R.356 SO4.25: 3 residues within 4Å: Chain C: Y.321 Chain I: D.286, K.290 1 PLIP interactions: 1 interactions with chain I Salt bridges: I:K.290 SO4.26: 5 residues within 4Å: Chain G: Q.326 Chain I: E.259, E.345, Y.346, K.347 3 PLIP interactions: 3 interactions with chain I Hydrogen bonds: I:E.345, I:K.347 Salt bridges: I:K.262 SO4.27: 5 residues within 4Å: Chain I: S.87, T.157, Q.248, Y.361, E.362 3 PLIP interactions: 3 interactions with chain I Hydrogen bonds: I:S.87, I:T.157, I:Y.361 SO4.29: 3 residues within 4Å: Chain J: V.84, Y.361, E.362 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:Y.361 SO4.30: 5 residues within 4Å: Chain J: E.19, L.22, T.24, V.78, K.347 2 PLIP interactions: 2 interactions with chain J Hydrogen bonds: J:T.24 Salt bridges: J:K.347

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Demmer, J.K. et al., Molecular basis of the flavin-based electron-bifurcating caffeyl-CoA reductase reaction. FEBS Lett. (2018)

Release Date

2018-01-24

Peptides

Caffeyl-CoA reductase-Etf complex subunit CarE: AEGK
Caffeyl-CoA reductase-Etf complex subunit CarD: BFHL
Caffeyl-CoA reductase-Etf complex subunit CarC: CDIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
E

G
A

K
E

B
B

F
F

H
B

L
F

C
C

D
D

I
C

J
D

Caffeyl-CoA reductase-Etf complex subunit CarE

Caffeyl-CoA reductase-Etf complex subunit CarD

Caffeyl-CoA reductase-Etf complex subunit CarC