SMTL ID : 4i42.1 (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

5 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.132, G.133, T.155, V.159, S.161, F.162, Q.189 Chain F: T.254, Y.258, F.270, K.273 Ligands: CL.4 26 PLIP interactions: 20 interactions with chain A, 6 interactions with chain F 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:G.133, A:S.161, A:F.162, F:K.273, F:K.273 Water bridges: A:R.45, A:R.45 Salt bridges: A:R.45, A:R.45, A:K.89, F:K.273 pi-Stacking: F:F.270, F:F.270 1HA.8: 30 residues within 4Å: Chain B: Q.43, V.44, R.45, A.47, F.48, 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 Chain D: T.254, Y.258, F.270, K.273 Chain F: M.1 Ligands: CL.14 31 PLIP interactions: 23 interactions with chain B, 6 interactions with chain D, 2 interactions with chain F Hydrophobic interactions: B:F.48, B:Y.97, B:L.106, 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:Y.129, B:G.133, B:T.155, B:S.161, B:F.162, D:K.273, D:K.273, F:M.1 Salt bridges: B:R.45, B:R.45, B:K.89, D:K.273 pi-Stacking: D:F.270, D:F.270 Water bridges: F:M.1 1HA.15: 29 residues within 4Å: Chain A: M.1 Chain C: Q.43, V.44, R.45, A.47, F.48, 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 Chain E: T.254, Y.258, F.270, K.273 Ligands: CL.23 28 PLIP interactions: 21 interactions with chain C, 6 interactions with chain E, 1 interactions with chain A Hydrophobic interactions: C:F.48, C:Y.97, C:L.106, C:V.108, C:L.109, C:Y.129, C:I.131, E:T.254 Hydrogen bonds: C:S.84, C:S.84, C:G.86, C:G.86, C:Q.88, C:Y.129, C:G.133, C:S.161, C:F.162, E:K.273, E:K.273, A:M.1 Water bridges: C:Q.43, C:R.45, C:R.45 Salt bridges: C:R.45, C:R.45, E:K.273 pi-Stacking: E:F.270, E:F.270 1HA.35: 29 residues within 4Å: Chain B: I.2 Chain C: T.254, Y.258, 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.44 28 PLIP interactions: 22 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:Y.129, E:G.133, E:T.155, E:S.161, E:F.162, C:K.273, C:K.273 Water bridges: E:D.163 Salt bridges: E:R.45, E:R.45, E:K.89, C:K.273 pi-Stacking: C:F.270, C:F.270 1HA.45: 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, F.48, 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 Ligands: CL.50 33 PLIP interactions: 25 interactions with chain F, 2 interactions with chain E, 6 interactions with chain A Hydrophobic interactions: F:F.48, 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:D.87, F:Q.88, F:K.89, F:Y.129, F:Y.129, F:G.133, F:T.155, F:S.161, F:F.162, E:M.1, A:K.273, A:K.273 Water bridges: F:R.45, F:R.45, E:M.1 Salt bridges: F:R.45, F:R.45, F:K.89, A:K.273 pi-Stacking: A:F.270, A:F.270

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

EDO.2: 1 residues within 4Å: Chain A: N.149 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.149 EDO.11: 5 residues within 4Å: Chain B: S.279, R.283 Chain C: D.32, N.68, L.222 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:R.283, C:L.222 EDO.19: 3 residues within 4Å: Chain C: F.22, Q.58 Ligands: EDO.21 3 PLIP interactions: 3 interactions with chain C Water bridges: C:C.18, C:Q.58, C:D.62 EDO.20: 5 residues within 4Å: Chain C: L.196, D.197, G.199 Chain D: D.197 Ligands: BTB.24 No protein-ligand interaction detected (PLIP) EDO.21: 5 residues within 4Å: Chain C: E.20, G.21, F.22, Q.58 Ligands: EDO.19 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.21 EDO.30: 5 residues within 4Å: Chain D: G.85, G.86, G.133 Ligands: SO4.31, BCT.32 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:G.86, D:G.133 Water bridges: D:S.161 EDO.39: 3 residues within 4Å: Chain E: R.26, A.77, G.78 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:R.26, E:R.26, E:G.78 EDO.40: 4 residues within 4Å: Chain E: K.80, Y.129, N.149, I.151 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.149 Water bridges: E:N.149 EDO.41: 4 residues within 4Å: Chain E: E.20, G.21, F.22, Q.58 No protein-ligand interaction detected (PLIP)

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

SO4.3: 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 SO4.12: 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 SO4.13: 2 residues within 4Å: Chain B: K.98, G.102 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.98 SO4.22: 5 residues within 4Å: Chain C: G.92, D.93, Y.94, K.98, H.104 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:D.93, C:Y.94 Salt bridges: C:K.98, C:H.104 SO4.31: 10 residues within 4Å: Chain D: G.132, G.133, Q.154, T.155, G.156, F.162, D.163, W.184 Ligands: EDO.30, BCT.32 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:G.133, D:Q.154, D:T.155, D:T.155, D:G.156, D:D.163 Water bridges: D:S.161, D:S.161, D:D.163 SO4.42: 4 residues within 4Å: Chain E: G.92, D.93, Y.94, H.104 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:D.93, E:Y.94 Salt bridges: E:K.98, E:H.104 SO4.43: 12 residues within 4Å: Chain B: A.172, R.173, I.174, G.176 Chain E: A.172, I.174, V.175, G.176 Chain F: A.172, I.174, G.176 Ligands: BTB.52 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:I.174, E:A.172 SO4.49: 5 residues within 4Å: Chain F: G.92, D.93, Y.94, K.98, H.104 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:D.93, F:Y.94 Water bridges: F:K.98, F:G.102 Salt bridges: F:K.98, F:H.104

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

CL.4: 6 residues within 4Å: Chain A: G.132, Q.154, T.155, G.156, W.184 Ligands: 1HA.1 Ligand excluded by PLIP CL.5: 2 residues within 4Å: Chain A: R.45, K.80 Ligand excluded by PLIP CL.6: 1 residues within 4Å: Ligands: BTB.24 Ligand excluded by PLIP CL.14: 6 residues within 4Å: Chain B: G.132, Q.154, T.155, G.156, W.184 Ligands: 1HA.8 Ligand excluded by PLIP CL.23: 6 residues within 4Å: Chain C: G.132, Q.154, T.155, G.156, W.184 Ligands: 1HA.15 Ligand excluded by PLIP CL.44: 6 residues within 4Å: Chain E: G.132, Q.154, T.155, G.156, W.184 Ligands: 1HA.35 Ligand excluded by PLIP CL.50: 6 residues within 4Å: Chain F: G.132, Q.154, T.155, G.156, W.184 Ligands: 1HA.45 Ligand excluded by PLIP CL.51: 3 residues within 4Å: Chain F: R.26, A.77, G.78 Ligand excluded by PLIP

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

BCT.7: 3 residues within 4Å: Chain A: R.26, A.77, G.78 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.26, A:G.78 BCT.32: 6 residues within 4Å: Chain B: Y.258 Chain D: G.133, S.161, F.162 Ligands: EDO.30, SO4.31 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:S.161 Water bridges: D:D.163 BCT.33: 2 residues within 4Å: Ligands: GOL.28, PEG.29 No protein-ligand interaction detected (PLIP) BCT.34: 2 residues within 4Å: Ligands: GOL.28, PEG.29 No protein-ligand interaction detected (PLIP) BCT.53: 4 residues within 4Å: Chain D: G.33, D.67, N.68 Chain F: R.283 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain F Hydrogen bonds: D:N.68, F:R.283

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 7 residues within 4Å: Chain B: Y.10, T.203, V.205, E.213, R.216, W.217 Chain E: R.188 6 PLIP interactions: 2 interactions with chain E, 4 interactions with chain B Hydrogen bonds: E:R.188, E:R.188, B:T.203, B:T.203, B:E.213, B:R.216 GOL.16: 6 residues within 4Å: Chain C: D.79, K.80, G.128, Y.129, N.149, I.151 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.80, C:N.149, C:N.149 GOL.17: 8 residues within 4Å: Chain C: Y.10, T.203, V.205, E.213, R.216, W.217 Chain D: R.188 Ligands: GOL.27 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:Y.10, C:T.203, C:E.213, C:R.216, D:R.188, D:R.188 GOL.25: 6 residues within 4Å: Chain A: R.188 Chain D: T.203, V.205, E.213, R.216, W.217 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:T.203, D:R.216, A:R.188, A:R.188 Water bridges: D:T.203, D:V.204 GOL.26: 6 residues within 4Å: Chain D: D.79, K.80, G.128, Y.129, N.149, I.151 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.80, D:N.149 GOL.27: 2 residues within 4Å: Chain D: Q.194 Ligands: GOL.17 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Q.194 Water bridges: D:R.188, D:R.188 GOL.28: 4 residues within 4Å: Chain D: R.45, Y.129 Ligands: BCT.33, BCT.34 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.45, D:R.45 GOL.36: 7 residues within 4Å: Chain E: Y.10, T.203, V.205, E.213, R.216, W.217 Chain F: R.188 5 PLIP interactions: 3 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:E.213, E:R.216, F:R.188, F:R.188 Water bridges: E:T.203 GOL.37: 7 residues within 4Å: Chain C: L.106, L.109 Chain E: R.230, E.248, G.251, N.252, M.255 10 PLIP interactions: 5 interactions with chain E, 2 interactions with chain A, 3 interactions with chain C Hydrogen bonds: E:R.230, E:R.230, E:N.252 Water bridges: E:R.64, E:Q.247, A:P.285, A:P.285, C:L.106, C:L.106, C:R.113 GOL.46: 5 residues within 4Å: Chain F: K.80, G.128, Y.129, N.149, I.151 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:K.80, F:N.149

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

PEG.10: 6 residues within 4Å: Chain B: P.50, K.54, D.99, H.105, N.107 Chain D: Y.65 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D Water bridges: B:K.54 Hydrogen bonds: D:Y.65 PEG.18: 5 residues within 4Å: Chain C: L.51, K.54, D.99, H.105 Chain E: Y.65 2 PLIP interactions: 2 interactions with chain C Water bridges: C:L.51, C:N.107 PEG.29: 9 residues within 4Å: Chain D: Q.43, V.44, R.45, A.47, S.84, G.86, Q.88 Ligands: BCT.33, BCT.34 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Q.43, D:S.84, D:G.86 PEG.38: 6 residues within 4Å: Chain C: Y.65 Chain E: P.50, K.54, D.99, H.105, N.107 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain C Water bridges: E:D.100, E:D.100, E:N.107 Hydrogen bonds: C:Y.65 PEG.47: 5 residues within 4Å: Chain A: Y.65 Chain F: P.50, K.54, D.99, H.105 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:K.54 PEG.48: 6 residues within 4Å: Chain A: L.51, K.54, D.99, H.105, N.107 Chain F: Y.65 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.54, A:N.107

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

BTB.24: 17 residues within 4Å: Chain A: I.174, V.175, G.176, K.179, D.197, M.198, G.199 Chain C: I.174, V.175, M.198, G.199 Chain D: I.174, D.197, M.198, G.199 Ligands: CL.6, EDO.20 7 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C, 3 interactions with chain A Hydrogen bonds: D:I.174, D:D.197, C:I.174, A:M.198 Water bridges: C:V.175, A:L.196, A:D.197 BTB.52: 14 residues within 4Å: Chain B: I.174, V.175, M.198 Chain E: I.174, V.175, D.197, M.198 Chain F: I.174, V.175, G.176, K.179, D.197, M.198 Ligands: SO4.43 4 PLIP interactions: 2 interactions with chain F, 1 interactions with chain B, 1 interactions with chain E Hydrogen bonds: F:I.174, F:D.197, B:M.198, E:I.174

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
A

B
B

C
C

D
D

E
E

F
F

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

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