SMTL ID : 4i4z.1 (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)

2NE.1: 23 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, V.98, Y.119, I.121, G.122, G.123, T.145, V.149, S.151, Q.179 Chain F: Y.248, F.260, K.263 Ligands: BCT.2 18 PLIP interactions: 15 interactions with chain A, 3 interactions with chain F Hydrophobic interactions: A:Y.87, A:V.98, A:Y.119, 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 Water bridges: A:D.153, A:Q.179 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: H.29, K.30, R.31, A.33, S.75, G.76, G.77, D.78, Q.79, Y.87, V.98, Y.119, I.121, G.123, T.145, V.149, S.151, F.152, Q.179 Chain D: Y.248, F.260, K.263 Ligands: BCT.4 21 PLIP interactions: 17 interactions with chain B, 4 interactions with chain D Hydrophobic interactions: B:Y.87, B:V.98, B:Y.119, B:Y.119, B:I.121 Hydrogen bonds: B:S.75, B:S.75, B:G.77, B:G.77, B:Q.79, B:G.123, B:T.145, B:S.151, D:K.263 Water bridges: B:Y.119, B:Q.179 Salt bridges: B:R.31, B:R.31, D:K.263 pi-Stacking: D:F.260, D:F.260 2NE.5: 22 residues within 4Å: Chain C: H.29, K.30, R.31, A.33, S.75, G.76, G.77, D.78, Q.79, Y.87, V.98, Y.119, I.121, G.123, T.145, V.149, S.151, Q.179 Chain E: Y.248, F.260, K.263 Ligands: BCT.6 19 PLIP interactions: 15 interactions with chain C, 4 interactions with chain E Hydrophobic interactions: C:Y.87, C:V.98, C:I.121, C:I.121 Hydrogen bonds: C:S.75, C:S.75, C:G.77, C:G.77, C:Q.79, C:G.123, C:S.151, E:K.263 Water bridges: C:Y.119, C:Q.179 Salt bridges: C:R.31, C:R.31, E:K.263 pi-Stacking: E:F.260, E:F.260 2NE.8: 22 residues within 4Å: Chain B: 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, V.98, Y.119, I.121, G.122, G.123, T.145, V.149, S.151, Q.179 Ligands: BCT.9 19 PLIP interactions: 14 interactions with chain D, 5 interactions with chain B Hydrophobic interactions: D:Y.87, D:V.98, D:Y.119, D:I.121 Hydrogen bonds: D:S.75, D:S.75, D:G.77, D:G.77, D:D.78, D:Q.79, D:G.123, B:K.263 Water bridges: D:D.153 Salt bridges: D:R.31, D:R.31, B:K.263, B:K.263 pi-Stacking: B:F.260, B:F.260 2NE.10: 22 residues within 4Å: Chain C: F.260, K.263 Chain E: H.29, K.30, 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, Q.179 Ligands: BCT.11 20 PLIP interactions: 17 interactions with chain E, 3 interactions with chain C Hydrophobic interactions: E:Y.87, E:V.98, E:Y.119, E:I.121 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, E:S.151 Water bridges: E:Y.119 Salt bridges: E:R.31, E:R.31, C:K.263 pi-Stacking: C:F.260, C:F.260 2NE.12: 25 residues within 4Å: Chain A: Y.248, F.260, K.263 Chain F: H.29, K.30, 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.13 18 PLIP interactions: 5 interactions with chain A, 13 interactions with chain F Hydrogen bonds: A:K.263, F:S.75, F:S.75, F:G.77, F:G.77, F:Q.79, F:Y.119, F:G.123, F:T.145 Salt bridges: A:K.263, A:K.263, F:R.31, F:R.31 pi-Stacking: A:F.260, A:F.260 Hydrophobic interactions: F:V.98, F:Y.119, F:I.121

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

BCT.2: 9 residues within 4Å: Chain A: G.122, G.123, Q.144, T.145, G.146, S.151, F.152, W.174 Ligands: 2NE.1 No protein-ligand interaction detected (PLIP) 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 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.122, B:Q.144, B:T.145, B:G.146, B:S.151 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 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.145, C:G.146 BCT.9: 9 residues within 4Å: Chain D: G.122, G.123, Q.144, T.145, G.146, S.151, F.152, W.174 Ligands: 2NE.8 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.145, D:G.146 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 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:G.122, E:Q.144, E:T.145, E:G.146, E:S.151 BCT.13: 8 residues within 4Å: Chain F: G.122, G.123, Q.144, T.145, G.146, S.151, W.174 Ligands: 2NE.12 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:G.122, F:Q.144, F:T.145, F:G.146

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

MLI.7: 10 residues within 4Å: Chain A: I.164, V.165, R.187, M.188 Chain C: I.164, V.165, M.188 Chain D: I.164, V.165, M.188 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D: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
A

B
B

C
C

D
D

E
E

F
F

Naphthoate synthase

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