SMTL ID : 8jyu.1

Acyl-ACP Synthetase structure bound to Decanoyl-AMP

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: T.175, M.320, S.321, E.322 Ligands: AMP.2 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:E.322, AMP.2 MG.4: 5 residues within 4Å: Chain B: T.175, M.320, S.321, E.322 Ligands: AMP.5 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:E.322, AMP.5 MG.7: 5 residues within 4Å: Chain C: T.175, M.320, S.321, E.322 Ligands: AMP.8 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Ligand interactions Metal complexes: C:E.322, AMP.8 MG.10: 5 residues within 4Å: Chain D: T.175, M.320, S.321, E.322 Ligands: AMP.11 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Ligand interactions Metal complexes: D:E.322, AMP.11 MG.13: 5 residues within 4Å: Chain E: T.175, M.320, S.321, E.322 Ligands: AMP.14 2 PLIP interactions: 1 interactions with chain E, 1 Ligand-Ligand interactions Metal complexes: E:E.322, AMP.14 MG.16: 5 residues within 4Å: Chain F: T.175, M.320, S.321, E.322 Ligands: AMP.17 2 PLIP interactions: 1 interactions with chain F, 1 Ligand-Ligand interactions Metal complexes: F:E.322, AMP.17

6 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.2: 17 residues within 4Å: Chain A: T.175, H.226, G.296, A.297, A.298, G.317, Y.318, G.319, M.320, S.321, T.409, D.411, I.423, R.426, K.522 Ligands: MG.1, DKA.3 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:T.175, A:G.296, A:G.317, A:G.319, A:S.321, A:D.411, A:R.426, A:K.522 Salt bridges: A:H.226, A:K.522 pi-Stacking: A:Y.318 AMP.5: 17 residues within 4Å: Chain B: T.175, H.226, G.296, A.297, A.298, G.317, Y.318, G.319, M.320, S.321, T.409, D.411, I.423, R.426, K.522 Ligands: MG.4, DKA.6 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:G.296, B:G.317, B:G.319, B:S.321, B:D.411, B:R.426, B:K.522 Salt bridges: B:H.226, B:K.522 pi-Stacking: B:Y.318 AMP.8: 17 residues within 4Å: Chain C: T.175, H.226, G.296, A.297, A.298, G.317, Y.318, G.319, M.320, S.321, T.409, D.411, I.423, R.426, K.522 Ligands: MG.7, DKA.9 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:G.296, C:G.317, C:G.319, C:S.321, C:D.411, C:R.426, C:K.522 Salt bridges: C:H.226, C:K.522 pi-Stacking: C:Y.318 AMP.11: 17 residues within 4Å: Chain D: T.175, H.226, G.296, A.297, A.298, G.317, Y.318, G.319, M.320, S.321, T.409, D.411, I.423, R.426, K.522 Ligands: MG.10, DKA.12 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:T.175, D:G.296, D:G.317, D:G.319, D:S.321, D:D.411, D:R.426, D:K.522 Salt bridges: D:H.226, D:K.522 pi-Stacking: D:Y.318 AMP.14: 17 residues within 4Å: Chain E: T.175, H.226, G.296, A.297, A.298, G.317, Y.318, G.319, M.320, S.321, T.409, D.411, I.423, R.426, K.522 Ligands: MG.13, DKA.15 11 PLIP interactions: 11 interactions with chain E Hydrogen bonds: E:T.175, E:G.296, E:G.317, E:G.319, E:S.321, E:D.411, E:R.426, E:K.522 Salt bridges: E:H.226, E:K.522 pi-Stacking: E:Y.318 AMP.17: 17 residues within 4Å: Chain F: T.175, H.226, G.296, A.297, A.298, G.317, Y.318, G.319, M.320, S.321, T.409, D.411, I.423, R.426, K.522 Ligands: MG.16, DKA.18 10 PLIP interactions: 10 interactions with chain F Hydrogen bonds: F:G.296, F:G.317, F:G.319, F:S.321, F:D.411, F:R.426, F:K.522 Salt bridges: F:H.226, F:K.522 pi-Stacking: F:Y.318

6 x DKA: DECANOIC ACID(Non-covalent)

DKA.3: 14 residues within 4Å: Chain A: H.226, W.230, V.293, G.295, G.296, G.317, Y.318, G.319, M.320, S.321, P.325, I.326, I.329 Ligands: AMP.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:W.230, A:W.230, A:V.293, A:P.325, A:I.326, A:I.326, A:I.329, A:I.329 Hydrogen bonds: A:S.321 Salt bridges: A:H.226, A:K.522 DKA.6: 14 residues within 4Å: Chain B: H.226, W.230, V.293, G.295, G.296, G.317, Y.318, G.319, M.320, S.321, P.325, I.326, I.329 Ligands: AMP.5 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:W.230, B:W.230, B:V.293, B:P.325, B:I.326, B:I.326, B:I.329, B:I.329 Hydrogen bonds: B:S.321 Salt bridges: B:H.226, B:K.522 DKA.9: 14 residues within 4Å: Chain C: H.226, W.230, V.293, G.295, G.296, G.317, Y.318, G.319, M.320, S.321, P.325, I.326, I.329 Ligands: AMP.8 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:W.230, C:W.230, C:V.293, C:P.325, C:I.326, C:I.326, C:I.329, C:I.329 Hydrogen bonds: C:S.321 Salt bridges: C:H.226, C:K.522 DKA.12: 14 residues within 4Å: Chain D: H.226, W.230, V.293, G.295, G.296, G.317, Y.318, G.319, M.320, S.321, P.325, I.326, I.329 Ligands: AMP.11 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:W.230, D:W.230, D:V.293, D:P.325, D:I.326, D:I.326, D:I.329, D:I.329 Hydrogen bonds: D:S.321 Salt bridges: D:H.226, D:K.522 DKA.15: 14 residues within 4Å: Chain E: H.226, W.230, V.293, G.295, G.296, G.317, Y.318, G.319, M.320, S.321, P.325, I.326, I.329 Ligands: AMP.14 11 PLIP interactions: 11 interactions with chain E Hydrophobic interactions: E:W.230, E:W.230, E:V.293, E:P.325, E:I.326, E:I.326, E:I.329, E:I.329 Hydrogen bonds: E:S.321 Salt bridges: E:H.226, E:K.522 DKA.18: 14 residues within 4Å: Chain F: H.226, W.230, V.293, G.295, G.296, G.317, Y.318, G.319, M.320, S.321, P.325, I.326, I.329 Ligands: AMP.17 11 PLIP interactions: 11 interactions with chain F Hydrophobic interactions: F:W.230, F:W.230, F:V.293, F:P.325, F:I.326, F:I.326, F:I.329, F:I.329 Hydrogen bonds: F:S.321 Salt bridges: F:H.226, F:K.522

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, H. et al., Acyl-ACP Synthetase structure bound to Decanoyl-AMP. To Be Published

Release Date

2024-07-10

Peptides

Acyl-acyl carrier protein synthetase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

C
B

D
C

E
E

F
F

Acyl-acyl carrier protein synthetase

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