SMTL ID : 3kbr.1

The crystal structure of cyclohexadienyl dehydratase precursor from Pseudomonas aeruginosa PA01

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.66 Å

Oligo State

homo-hexamer

Ligands

6 x NI: NICKEL (II) ION(Non-covalent)

NI.1: 4 residues within 4Å: Chain A: E.112, H.191 Chain E: H.234 Ligands: CL.2 5 PLIP interactions: 1 interactions with chain E, 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: E:H.234, A:E.112, A:E.112, A:H.191, H2O.31 NI.11: 4 residues within 4Å: Chain B: E.112, H.191 Chain D: H.234 Ligands: CL.12 5 PLIP interactions: 1 interactions with chain D, 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: D:H.234, B:E.112, B:E.112, B:H.191, H2O.25 NI.21: 4 residues within 4Å: Chain C: E.112, H.191 Chain F: H.234 Ligands: CL.22 5 PLIP interactions: 1 interactions with chain F, 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: F:H.234, C:E.112, C:E.112, C:H.191, H2O.37 NI.31: 4 residues within 4Å: Chain B: H.234 Chain D: E.112, H.191 Ligands: CL.32 5 PLIP interactions: 3 interactions with chain D, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: D:E.112, D:E.112, D:H.191, B:H.234, H2O.12 NI.41: 4 residues within 4Å: Chain A: H.234 Chain E: E.112, H.191 Ligands: CL.42 5 PLIP interactions: 3 interactions with chain E, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: E:E.112, E:E.112, E:H.191, A:H.234, H2O.6 NI.51: 4 residues within 4Å: Chain C: H.234 Chain F: E.112, H.191 Ligands: CL.52 5 PLIP interactions: 3 interactions with chain F, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: F:E.112, F:E.112, F:H.191, C:H.234, H2O.19

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

CL.2: 6 residues within 4Å: Chain A: E.112, C.188, A.189, H.191 Chain E: H.234 Ligands: NI.1 Ligand excluded by PLIP CL.12: 6 residues within 4Å: Chain B: E.112, C.188, A.189, H.191 Chain D: H.234 Ligands: NI.11 Ligand excluded by PLIP CL.22: 6 residues within 4Å: Chain C: E.112, C.188, A.189, H.191 Chain F: H.234 Ligands: NI.21 Ligand excluded by PLIP CL.32: 6 residues within 4Å: Chain B: H.234 Chain D: E.112, C.188, A.189, H.191 Ligands: NI.31 Ligand excluded by PLIP CL.42: 6 residues within 4Å: Chain A: H.234 Chain E: E.112, C.188, A.189, H.191 Ligands: NI.41 Ligand excluded by PLIP CL.52: 6 residues within 4Å: Chain C: H.234 Chain F: E.112, C.188, A.189, H.191 Ligands: NI.51 Ligand excluded by PLIP

30 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: K.103, D.197, F.198, A.199 Ligand excluded by PLIP GOL.4: 5 residues within 4Å: Chain A: E.5, S.6, D.9, R.10, E.13 Ligand excluded by PLIP GOL.5: 6 residues within 4Å: Chain A: E.5, S.6, R.207, D.208, E.209, A.210 Ligand excluded by PLIP GOL.7: 5 residues within 4Å: Chain A: L.12, E.13, S.14, G.15, G.53 Ligand excluded by PLIP GOL.8: 5 residues within 4Å: Chain A: L.150, V.151, H.152, P.153, Q.161 Ligand excluded by PLIP GOL.13: 4 residues within 4Å: Chain B: K.103, D.197, F.198, A.199 Ligand excluded by PLIP GOL.14: 5 residues within 4Å: Chain B: E.5, S.6, D.9, R.10, E.13 Ligand excluded by PLIP GOL.15: 6 residues within 4Å: Chain B: E.5, S.6, R.207, D.208, E.209, A.210 Ligand excluded by PLIP GOL.17: 5 residues within 4Å: Chain B: L.12, E.13, S.14, G.15, G.53 Ligand excluded by PLIP GOL.18: 5 residues within 4Å: Chain B: L.150, V.151, H.152, P.153, Q.161 Ligand excluded by PLIP GOL.23: 4 residues within 4Å: Chain C: K.103, D.197, F.198, A.199 Ligand excluded by PLIP GOL.24: 5 residues within 4Å: Chain C: E.5, S.6, D.9, R.10, E.13 Ligand excluded by PLIP GOL.25: 6 residues within 4Å: Chain C: E.5, S.6, R.207, D.208, E.209, A.210 Ligand excluded by PLIP GOL.27: 5 residues within 4Å: Chain C: L.12, E.13, S.14, G.15, G.53 Ligand excluded by PLIP GOL.28: 5 residues within 4Å: Chain C: L.150, V.151, H.152, P.153, Q.161 Ligand excluded by PLIP GOL.33: 4 residues within 4Å: Chain D: K.103, D.197, F.198, A.199 Ligand excluded by PLIP GOL.34: 5 residues within 4Å: Chain D: E.5, S.6, D.9, R.10, E.13 Ligand excluded by PLIP GOL.35: 6 residues within 4Å: Chain D: E.5, S.6, R.207, D.208, E.209, A.210 Ligand excluded by PLIP GOL.37: 5 residues within 4Å: Chain D: L.12, E.13, S.14, G.15, G.53 Ligand excluded by PLIP GOL.38: 5 residues within 4Å: Chain D: L.150, V.151, H.152, P.153, Q.161 Ligand excluded by PLIP GOL.43: 4 residues within 4Å: Chain E: K.103, D.197, F.198, A.199 Ligand excluded by PLIP GOL.44: 5 residues within 4Å: Chain E: E.5, S.6, D.9, R.10, E.13 Ligand excluded by PLIP GOL.45: 6 residues within 4Å: Chain E: E.5, S.6, R.207, D.208, E.209, A.210 Ligand excluded by PLIP GOL.47: 5 residues within 4Å: Chain E: L.12, E.13, S.14, G.15, G.53 Ligand excluded by PLIP GOL.48: 5 residues within 4Å: Chain E: L.150, V.151, H.152, P.153, Q.161 Ligand excluded by PLIP GOL.53: 4 residues within 4Å: Chain F: K.103, D.197, F.198, A.199 Ligand excluded by PLIP GOL.54: 5 residues within 4Å: Chain F: E.5, S.6, D.9, R.10, E.13 Ligand excluded by PLIP GOL.55: 6 residues within 4Å: Chain F: E.5, S.6, R.207, D.208, E.209, A.210 Ligand excluded by PLIP GOL.57: 5 residues within 4Å: Chain F: L.12, E.13, S.14, G.15, G.53 Ligand excluded by PLIP GOL.58: 5 residues within 4Å: Chain F: L.150, V.151, H.152, P.153, Q.161 Ligand excluded by PLIP

12 x FMT: FORMIC ACID(Non-functional Binders)

FMT.6: 4 residues within 4Å: Chain A: P.192, Q.193, P.195 Ligands: FMT.36 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.195, A:P.195 FMT.9: 3 residues within 4Å: Chain A: R.229, M.232, E.233 No protein-ligand interaction detected (PLIP) FMT.16: 4 residues within 4Å: Chain B: P.192, Q.193, P.195 Ligands: FMT.56 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:P.195, B:P.195 FMT.19: 3 residues within 4Å: Chain B: R.229, M.232, E.233 No protein-ligand interaction detected (PLIP) FMT.26: 4 residues within 4Å: Chain C: P.192, Q.193, P.195 Ligands: FMT.46 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:P.195, C:P.195 FMT.29: 3 residues within 4Å: Chain C: R.229, M.232, E.233 No protein-ligand interaction detected (PLIP) FMT.36: 4 residues within 4Å: Chain D: P.192, Q.193, P.195 Ligands: FMT.6 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:P.195 FMT.39: 3 residues within 4Å: Chain D: R.229, M.232, E.233 No protein-ligand interaction detected (PLIP) FMT.46: 4 residues within 4Å: Chain E: P.192, Q.193, P.195 Ligands: FMT.26 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:P.195 FMT.49: 3 residues within 4Å: Chain E: R.229, M.232, E.233 No protein-ligand interaction detected (PLIP) FMT.56: 4 residues within 4Å: Chain F: P.192, Q.193, P.195 Ligands: FMT.16 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:P.195 FMT.59: 3 residues within 4Å: Chain F: R.229, M.232, E.233 No protein-ligand interaction detected (PLIP)

6 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.10: 13 residues within 4Å: Chain A: D.24, Y.25, W.63, G.81, I.82, S.83, R.88, K.103, T.135, N.155, D.173, E.176, K.201 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:S.83, A:T.135, A:T.135, A:N.155 Water bridges: A:S.83, A:K.103, A:N.131, A:N.131, A:T.135 Salt bridges: A:D.24, A:R.88, A:K.103, A:D.173, A:E.176, A:K.201 pi-Cation interactions: A:Y.25 EPE.20: 13 residues within 4Å: Chain B: D.24, Y.25, W.63, G.81, I.82, S.83, R.88, K.103, T.135, N.155, D.173, E.176, K.201 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:S.83, B:T.135, B:T.135, B:N.155 Water bridges: B:S.83, B:K.103, B:N.131, B:N.131, B:T.135 Salt bridges: B:D.24, B:R.88, B:K.103, B:D.173, B:E.176, B:K.201 pi-Cation interactions: B:Y.25 EPE.30: 13 residues within 4Å: Chain C: D.24, Y.25, W.63, G.81, I.82, S.83, R.88, K.103, T.135, N.155, D.173, E.176, K.201 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:S.83, C:T.135, C:T.135, C:N.155 Water bridges: C:S.83, C:K.103, C:N.131, C:N.131, C:T.135 Salt bridges: C:D.24, C:R.88, C:K.103, C:D.173, C:E.176, C:K.201 pi-Cation interactions: C:Y.25 EPE.40: 13 residues within 4Å: Chain D: D.24, Y.25, W.63, G.81, I.82, S.83, R.88, K.103, T.135, N.155, D.173, E.176, K.201 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:S.83, D:T.135, D:N.155 Water bridges: D:S.83, D:K.103, D:N.131, D:N.131, D:T.135 Salt bridges: D:D.24, D:R.88, D:K.103, D:D.173, D:E.176, D:K.201 pi-Cation interactions: D:Y.25 EPE.50: 13 residues within 4Å: Chain E: D.24, Y.25, W.63, G.81, I.82, S.83, R.88, K.103, T.135, N.155, D.173, E.176, K.201 15 PLIP interactions: 15 interactions with chain E Hydrogen bonds: E:S.83, E:T.135, E:N.155 Water bridges: E:S.83, E:K.103, E:N.131, E:N.131, E:T.135 Salt bridges: E:D.24, E:R.88, E:K.103, E:D.173, E:E.176, E:K.201 pi-Cation interactions: E:Y.25 EPE.60: 13 residues within 4Å: Chain F: D.24, Y.25, W.63, G.81, I.82, S.83, R.88, K.103, T.135, N.155, D.173, E.176, K.201 15 PLIP interactions: 15 interactions with chain F Hydrogen bonds: F:S.83, F:T.135, F:N.155 Water bridges: F:S.83, F:K.103, F:N.131, F:N.131, F:T.135 Salt bridges: F:D.24, F:R.88, F:K.103, F:D.173, F:E.176, F:K.201 pi-Cation interactions: F:Y.25

Links

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Citation

Tan, K. et al., The crystal structure of cyclohexadienyl dehydratase precursor from Pseudomonas aeruginosa PA01. To be Published

Release Date

2009-11-10

Peptides

Cyclohexadienyl dehydratase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

Cyclohexadienyl dehydratase