SMTL ID : 4i4z.2 (1 other biounit)

Synechocystis sp. PCC 6803 1,4-dihydroxy-2-naphthoyl-coenzyme A synthase (MenB) in complex with salicylyl-CoA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-hexamer

Ligands

6 x 2NE: Salicylyl CoA(Non-covalent)(Covalent)

2NE.1: 21 residues within 4Å: Chain A: H.29, K.30, R.31, A.33, S.75, G.76, G.77, D.78, Q.79, Y.87, Y.119, I.121, G.123, T.145, V.149, S.151, Q.179 Chain F: Y.248, F.260, K.263 Ligands: BCT.2 17 PLIP interactions: 14 interactions with chain A, 3 interactions with chain F Hydrophobic interactions: A:Y.87, A:Y.119, A:Y.119, A:I.121, A:I.121 Hydrogen bonds: A:S.75, A:S.75, A:G.77, A:G.77, A:D.78, A:Q.79, A:G.123 Salt bridges: A:R.31, A:R.31, F:K.263 pi-Stacking: F:F.260, F:F.260 2NE.3: 23 residues within 4Å: Chain B: R.31, A.33, S.75, G.76, G.77, D.78, Q.79, Y.87, V.98, Y.119, I.121, G.122, G.123, T.145, V.149, S.151, F.152, D.153, Q.179 Chain E: Y.248, F.260, K.263 Ligands: BCT.4 18 PLIP interactions: 14 interactions with chain B, 4 interactions with chain E Hydrophobic interactions: B:Y.87, B:V.98, B:Y.119, B:Y.119, B:I.121, B:D.153 Hydrogen bonds: B:S.75, B:S.75, B:G.77, B:G.77, B:Q.79, B:G.123, E:K.263 Salt bridges: B:R.31, B:R.31, E:K.263 pi-Stacking: E:F.260, E:F.260 2NE.5: 24 residues within 4Å: Chain C: H.29, K.30, R.31, A.33, F.34, K.70, S.75, G.76, G.77, D.78, Q.79, Y.87, V.98, Y.119, G.122, G.123, T.145, V.149, S.151, Q.179 Chain D: Y.248, F.260, K.263 Ligands: BCT.6 20 PLIP interactions: 3 interactions with chain D, 17 interactions with chain C Salt bridges: D:K.263, C:R.31, C:R.31, C:K.70 pi-Stacking: D:F.260, D:F.260 Hydrophobic interactions: C:F.34, C:Y.87, C:V.98, C:Y.119 Hydrogen bonds: C:S.75, C:S.75, C:G.77, C:G.77, C:D.78, C:Q.79, C:G.123, C:S.151 Water bridges: C:H.29, C:D.153 2NE.8: 21 residues within 4Å: Chain C: Y.248, F.260, K.263 Chain D: H.29, K.30, R.31, A.33, S.75, G.76, G.77, D.78, Q.79, Y.87, Y.119, I.121, G.123, T.145, V.149, S.151, Q.179 Ligands: BCT.9 18 PLIP interactions: 15 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:Y.87, D:Y.119, D:Y.119, D:I.121, D:I.121 Hydrogen bonds: D:S.75, D:S.75, D:G.77, D:G.77, D:Q.79, D:Y.119, D:G.123, D:T.145 Salt bridges: D:R.31, D:R.31, C:K.263 pi-Stacking: C:F.260, C:F.260 2NE.10: 23 residues within 4Å: Chain B: Y.248, F.260, K.263 Chain E: R.31, A.33, S.75, G.76, G.77, D.78, Q.79, Y.87, V.98, Y.119, I.121, G.122, G.123, T.145, V.149, S.151, F.152, D.153, Q.179 Ligands: BCT.11 20 PLIP interactions: 17 interactions with chain E, 3 interactions with chain B Hydrophobic interactions: E:Y.87, E:V.98, E:Y.119, E:Y.119, E:I.121, E:D.153 Hydrogen bonds: E:S.75, E:S.75, E:G.77, E:G.77, E:D.78, E:Q.79, E:Y.119, E:G.123, E:T.145 Salt bridges: E:R.31, E:R.31, B:K.263 pi-Stacking: B:F.260, B:F.260 2NE.12: 24 residues within 4Å: Chain A: Y.248, F.260, K.263 Chain F: H.29, K.30, R.31, A.33, F.34, K.70, S.75, G.76, G.77, D.78, Q.79, Y.87, V.98, Y.119, G.122, G.123, T.145, V.149, S.151, Q.179 Ligands: BCT.13 20 PLIP interactions: 17 interactions with chain F, 3 interactions with chain A Hydrophobic interactions: F:F.34, F:Y.87, F:V.98, F:Y.119 Hydrogen bonds: F:S.75, F:S.75, F:G.77, F:G.77, F:Q.79, F:Y.119, F:G.123, F:T.145, F:S.151 Water bridges: F:H.29 Salt bridges: F:R.31, F:R.31, F:K.70, A:K.263 pi-Stacking: A:F.260, A:F.260

6 x BCT: BICARBONATE ION(Non-functional Binders)

BCT.2: 8 residues within 4Å: Chain A: G.122, G.123, Q.144, T.145, G.146, S.151, W.174 Ligands: 2NE.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.144, A:S.151 BCT.4: 9 residues within 4Å: Chain B: G.122, G.123, Q.144, T.145, G.146, S.151, F.152, W.174 Ligands: 2NE.3 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.146 BCT.6: 9 residues within 4Å: Chain C: G.122, G.123, Q.144, T.145, G.146, S.151, F.152, W.174 Ligands: 2NE.5 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.145 BCT.9: 8 residues within 4Å: Chain D: G.122, G.123, Q.144, T.145, G.146, S.151, W.174 Ligands: 2NE.8 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.144, D:S.151 BCT.11: 9 residues within 4Å: Chain E: G.122, G.123, Q.144, T.145, G.146, S.151, F.152, W.174 Ligands: 2NE.10 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:G.146 BCT.13: 9 residues within 4Å: Chain F: G.122, G.123, Q.144, T.145, G.146, S.151, F.152, W.174 Ligands: 2NE.12 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:T.145

2 x MLI: MALONATE ION(Non-functional Binders)

MLI.7: 9 residues within 4Å: Chain A: M.188 Chain B: I.164, R.187, M.188, G.189 Chain C: I.164, R.187, M.188, G.189 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Water bridges: A:V.165, A:M.188 Hydrogen bonds: B:M.188 MLI.14: 9 residues within 4Å: Chain D: M.188 Chain E: I.164, R.187, M.188, G.189 Chain F: I.164, R.187, M.188, G.189 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain E Water bridges: D:V.165, D:M.188 Hydrogen bonds: E:M.188

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sun, Y. et al., Structural basis of the induced-fit mechanism of 1,4-dihydroxy-2-naphthoyl coenzyme a synthase from the crotonase fold superfamily. Plos One (2013)

Release Date

2013-05-08

Peptides

Naphthoate synthase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

C
I

D
G

E
H

F
I

Naphthoate synthase

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