SMTL ID : 4i42.2 (1 other biounit)

E.coli. 1,4-dihydroxy-2-naphthoyl coenzyme A synthase (ecMenB) in complex with 1-hydroxy-2-naphthoyl-CoA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-hexamer

Ligands

6 x 1HA: 1-hydroxy-2-naphthoyl-CoA(Non-covalent)

1HA.1: 28 residues within 4Å: Chain A: Q.43, V.44, R.45, A.47, S.84, G.85, G.86, D.87, Q.88, K.89, Y.97, L.106, V.108, L.109, Y.129, I.131, G.133, T.155, V.159, S.161, F.162, Q.189 Chain D: M.1 Chain F: T.254, Y.258, F.270, K.273 Ligands: CL.8 32 PLIP interactions: 23 interactions with chain A, 7 interactions with chain F, 2 interactions with chain D Hydrophobic interactions: A:Y.97, A:L.106, A:V.108, A:L.109, A:Y.129, A:I.131, F:T.254 Hydrogen bonds: A:S.84, A:S.84, A:G.86, A:G.86, A:Q.88, A:K.89, A:Y.129, A:Y.129, A:G.133, A:T.155, A:S.161, A:F.162, F:K.273, F:K.273, D:M.1 Water bridges: A:R.45, A:R.45, F:K.273, D:M.1 Salt bridges: A:R.45, A:R.45, A:K.89, F:K.273 pi-Stacking: F:F.270, F:F.270 1HA.9: 28 residues within 4Å: Chain B: Q.43, V.44, R.45, A.47, S.84, G.85, G.86, D.87, Q.88, K.89, Y.97, V.108, L.109, Y.129, I.131, G.132, G.133, T.155, V.159, S.161, F.162, Q.189 Chain D: T.254, Y.258, F.270, K.273 Chain F: M.1 Ligands: CL.17 28 PLIP interactions: 21 interactions with chain B, 6 interactions with chain D, 1 interactions with chain F Hydrophobic interactions: B:V.108, B:L.109, B:Y.129, B:I.131, D:T.254 Hydrogen bonds: B:S.84, B:S.84, B:G.86, B:G.86, B:D.87, B:Q.88, B:K.89, B:Y.129, B:G.133, B:S.161, B:F.162, D:K.273, D:K.273, F:M.1 Water bridges: B:Y.129, B:D.163, B:Q.189 Salt bridges: B:R.45, B:R.45, B:K.89, D:K.273 pi-Stacking: D:F.270, D:F.270 1HA.18: 28 residues within 4Å: Chain A: M.1 Chain C: Q.43, V.44, R.45, A.47, S.84, G.85, G.86, D.87, Q.88, K.89, Y.97, V.108, L.109, Y.129, I.131, G.132, G.133, T.155, V.159, S.161, F.162, Q.189 Chain E: T.254, Y.258, F.270, K.273 Ligands: CL.24 30 PLIP interactions: 1 interactions with chain A, 23 interactions with chain C, 6 interactions with chain E Hydrogen bonds: A:M.1, C:S.84, C:S.84, C:G.86, C:G.86, C:D.87, C:Q.88, C:K.89, C:Y.129, C:Y.129, C:G.133, C:T.155, C:S.161, C:F.162, E:K.273, E:K.273 Hydrophobic interactions: C:Y.97, C:V.108, C:L.109, C:Y.129, C:I.131, E:T.254 Water bridges: C:R.45, C:R.45 Salt bridges: C:R.45, C:R.45, C:K.89, E:K.273 pi-Stacking: E:F.270, E:F.270 1HA.28: 28 residues within 4Å: Chain B: T.254, Y.258, F.270, K.273 Chain C: M.1 Chain D: Q.43, V.44, R.45, A.47, S.84, G.85, G.86, D.87, Q.88, Y.97, L.106, V.108, L.109, Y.129, I.131, G.132, G.133, T.155, V.159, S.161, F.162, Q.189 Ligands: CL.32 24 PLIP interactions: 19 interactions with chain D, 1 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: D:L.106, D:V.108, D:L.109, D:Y.129, D:Y.129, D:I.131, B:T.254 Hydrogen bonds: D:S.84, D:S.84, D:G.86, D:G.86, D:Q.88, D:Y.129, D:Y.129, D:G.133, D:T.155, D:S.161, D:F.162, C:M.1 Salt bridges: D:R.45, D:R.45, B:K.273 pi-Stacking: B:F.270, B:F.270 1HA.36: 27 residues within 4Å: Chain C: T.254, F.270, K.273 Chain E: Q.43, V.44, R.45, A.47, S.84, G.85, G.86, D.87, Q.88, K.89, Y.97, L.106, V.108, L.109, Y.129, I.131, G.132, G.133, T.155, V.159, S.161, F.162, Q.189 Ligands: CL.40 27 PLIP interactions: 21 interactions with chain E, 6 interactions with chain C Hydrophobic interactions: E:Y.97, E:L.106, E:V.108, E:L.109, E:Y.129, E:I.131, C:T.254 Hydrogen bonds: E:S.84, E:S.84, E:G.86, E:G.86, E:Q.88, E:K.89, E:Y.129, E:G.133, E:S.161, E:F.162, C:K.273, C:K.273 Water bridges: E:R.45, E:R.45 Salt bridges: E:R.45, E:R.45, E:K.89, C:K.273 pi-Stacking: C:F.270, C:F.270 1HA.41: 29 residues within 4Å: Chain A: T.254, Y.258, F.270, K.273 Chain E: M.1 Chain F: Q.43, V.44, R.45, A.47, S.84, G.85, G.86, D.87, Q.88, K.89, Y.97, L.106, V.108, L.109, Y.129, I.131, G.132, G.133, T.155, V.159, S.161, F.162, Q.189 Ligands: CL.48 30 PLIP interactions: 23 interactions with chain F, 6 interactions with chain A, 1 interactions with chain E Hydrophobic interactions: F:Y.97, F:L.106, F:V.108, F:L.109, F:Y.129, F:I.131, A:T.254 Hydrogen bonds: F:S.84, F:S.84, F:G.86, F:G.86, F:Q.88, F:K.89, F:Y.129, F:G.133, F:S.161, F:F.162, A:K.273, A:K.273, E:M.1 Water bridges: F:R.45, F:R.45, F:R.45, F:R.45 Salt bridges: F:R.45, F:R.45, F:K.89, A:K.273 pi-Stacking: A:F.270, A:F.270

11 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: R.173, D.239, C.240 Chain C: R.173 Chain F: Q.243 9 PLIP interactions: 1 interactions with chain F, 1 interactions with chain D, 2 interactions with chain C, 5 interactions with chain A Hydrogen bonds: F:Q.243, D:R.173, C:R.173, A:R.173, A:R.173, A:C.240 Water bridges: C:D.239, A:D.239, A:D.239 GOL.3: 7 residues within 4Å: Chain A: Y.10, T.203, V.205, E.213, R.216, W.217 Chain C: R.188 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:T.203, A:E.213, A:R.216, A:R.216, C:R.188, C:R.188 GOL.10: 6 residues within 4Å: Chain B: I.174, M.198 Chain E: I.174, V.175, M.198 Chain F: V.175 3 PLIP interactions: 1 interactions with chain F, 1 interactions with chain E, 1 interactions with chain B Hydrogen bonds: F:M.198, E:M.198, B:M.198 GOL.11: 6 residues within 4Å: Chain B: T.203, V.205, E.213, R.216, W.217 Chain E: R.188 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain E Hydrogen bonds: B:Y.10, B:T.203, B:R.216, E:R.188, E:R.188 GOL.19: 3 residues within 4Å: Chain C: K.80, N.149 Ligands: GOL.20 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.80, C:N.149 GOL.20: 6 residues within 4Å: Chain C: K.80, G.128, Y.129, N.149, I.151 Ligands: GOL.19 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.80 Water bridges: C:D.148 GOL.29: 6 residues within 4Å: Chain A: D.197 Chain D: L.196, D.197, M.198, G.199 Ligands: BTB.26 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:D.197 Water bridges: D:D.197, D:D.197, A:K.179 GOL.30: 5 residues within 4Å: Chain D: K.80, G.128, Y.129, N.149, I.151 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:K.80, D:N.149, D:N.149 GOL.31: 7 residues within 4Å: Chain A: R.188 Chain D: Y.10, T.203, V.205, E.213, R.216, W.217 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:T.203, D:E.213, D:R.216, A:R.188, A:R.188 Water bridges: D:T.203, D:V.204 GOL.37: 2 residues within 4Å: Chain E: N.149, L.207 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.149 GOL.42: 2 residues within 4Å: Chain F: D.148, N.149 1 PLIP interactions: 1 interactions with chain F Water bridges: F:D.148

9 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 2 residues within 4Å: Chain A: A.77, G.78 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.78 EDO.5: 4 residues within 4Å: Chain A: P.50, K.54, D.99, H.105 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.54 EDO.6: 4 residues within 4Å: Chain A: R.283 Chain E: D.32, N.68, L.222 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:N.68, A:R.283 Water bridges: E:L.222 EDO.13: 4 residues within 4Å: Chain B: L.196, D.197 Chain E: D.197, M.198 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain B Water bridges: E:K.179 Hydrogen bonds: B:D.197 EDO.14: 5 residues within 4Å: Chain B: K.80, G.128, Y.129, N.149, I.151 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.149 EDO.22: 2 residues within 4Å: Chain C: R.45, K.80 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.45, C:R.45 Water bridges: C:K.80 EDO.44: 6 residues within 4Å: Chain F: K.80, G.128, Y.129, N.149, I.151 Ligands: EDO.47 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:N.149, F:N.149 EDO.45: 3 residues within 4Å: Chain E: Y.3 Chain F: R.188, Q.189 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:Q.189 EDO.47: 3 residues within 4Å: Chain F: D.79, N.149 Ligands: EDO.44 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:N.149 Water bridges: F:D.79

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

SO4.7: 5 residues within 4Å: Chain A: G.92, D.93, Y.94, K.98, H.104 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.93, A:Y.94 Salt bridges: A:K.98, A:H.104 SO4.15: 5 residues within 4Å: Chain B: G.92, D.93, Y.94, K.98, H.104 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.93, B:Y.94 Salt bridges: B:K.98, B:H.104 SO4.16: 11 residues within 4Å: Chain B: A.172, R.173, V.175, G.176 Chain E: A.172, I.174, G.176 Chain F: A.172, R.173, I.174, G.176 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:R.173, E:A.172 SO4.23: 5 residues within 4Å: Chain C: G.92, D.93, Y.94, K.98, H.104 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:D.93, C:Y.94 Water bridges: C:K.98 Salt bridges: C:K.98, C:H.104 SO4.46: 5 residues within 4Å: Chain F: G.92, D.93, Y.94, K.98, H.104 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:D.93, F:Y.94 Salt bridges: F:K.98, F:H.104

11 x CL: CHLORIDE ION(Non-functional Binders)

CL.8: 6 residues within 4Å: Chain A: G.132, Q.154, T.155, G.156, W.184 Ligands: 1HA.1 Ligand excluded by PLIP CL.17: 6 residues within 4Å: Chain B: G.132, Q.154, T.155, G.156, W.184 Ligands: 1HA.9 Ligand excluded by PLIP CL.24: 6 residues within 4Å: Chain C: G.132, Q.154, T.155, G.156, W.184 Ligands: 1HA.18 Ligand excluded by PLIP CL.25: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.32: 6 residues within 4Å: Chain D: G.132, Q.154, T.155, G.156, W.184 Ligands: 1HA.28 Ligand excluded by PLIP CL.33: 2 residues within 4Å: Chain D: D.93, H.104 Ligand excluded by PLIP CL.34: 1 residues within 4Å: Ligands: BTB.26 Ligand excluded by PLIP CL.39: 3 residues within 4Å: Chain E: D.93, K.98, H.104 Ligand excluded by PLIP CL.40: 6 residues within 4Å: Chain E: G.132, Q.154, T.155, G.156, W.184 Ligands: 1HA.36 Ligand excluded by PLIP CL.48: 6 residues within 4Å: Chain F: G.132, Q.154, T.155, G.156, W.184 Ligands: 1HA.41 Ligand excluded by PLIP CL.49: 4 residues within 4Å: Chain B: R.188 Chain F: E.213, R.216, W.217 Ligand excluded by PLIP

4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.12: 5 residues within 4Å: Chain B: K.54, D.99, H.105, N.107 Chain D: Y.65 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Y.65 PEG.21: 7 residues within 4Å: Chain C: P.50, L.51, K.54, D.99, H.105, N.107 Chain E: Y.65 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:Y.65 PEG.38: 5 residues within 4Å: Chain C: Y.65 Chain E: P.50, K.54, H.105, N.107 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:N.107 Water bridges: E:D.100, E:D.100 PEG.43: 6 residues within 4Å: Chain A: Y.65 Chain F: P.50, K.54, D.99, H.105, N.107 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:K.54 Water bridges: F:D.100, F:D.100, F:N.107

1 x BTB: 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

BTB.26: 13 residues within 4Å: Chain A: I.174, V.175, G.176, D.197 Chain C: I.174, V.175, K.179, D.197, M.198 Chain D: I.174, M.198 Ligands: GOL.29, CL.34 4 PLIP interactions: 2 interactions with chain D, 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: D:I.174, D:V.175, A:D.197, C:M.198

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

BCT.27: 3 residues within 4Å: Chain C: R.26, A.77, G.78 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.26 Water bridges: C:G.76 BCT.35: 3 residues within 4Å: Chain D: R.26, A.77, G.78 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.26, D:R.26

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

1,4-Dihydroxy-2-naphthoyl-CoA synthase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

C
I

D
J

E
K

F
L

1,4-Dihydroxy-2-naphthoyl-CoA synthase

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