SMTL ID : 7w61.1

Crystal structure of farnesol dehydrogenase from Helicoverpa armigera

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-tetramer

Ligands

4 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.1: 31 residues within 4Å: Chain A: G.15, A.16, S.17, S.18, G.19, I.20, A.39, R.40, R.41, C.63, D.64, V.65, N.91, A.92, G.93, I.94, I.119, I.147, N.148, S.149, Y.164, K.168, P.196, G.197, L.198, V.199, T.201, A.202, M.203, V.205 Ligands: ACT.7 28 PLIP interactions: 28 interactions with chain A Hydrophobic interactions: A:P.196 Hydrogen bonds: A:G.15, A:G.15, A:S.17, A:S.17, A:S.18, A:I.20, A:R.40, A:R.41, A:D.64, A:V.65, A:N.91, A:G.93, A:Y.164, A:K.168, A:G.197, A:V.199, A:T.201, A:T.201, A:A.202, A:M.203 Water bridges: A:G.21, A:R.41, A:R.41, A:S.66, A:N.91 Salt bridges: A:R.40, A:R.41 NAP.9: 31 residues within 4Å: Chain B: G.15, A.16, S.17, S.18, G.19, I.20, A.39, R.40, R.41, C.63, D.64, V.65, N.91, A.92, G.93, I.94, I.119, I.147, N.148, S.149, Y.164, K.168, P.196, G.197, L.198, V.199, T.201, A.202, M.203, V.205 Ligands: ACT.15 28 PLIP interactions: 28 interactions with chain B Hydrophobic interactions: B:P.196 Hydrogen bonds: B:G.15, B:G.15, B:S.17, B:S.17, B:S.18, B:I.20, B:R.40, B:R.41, B:D.64, B:V.65, B:N.91, B:G.93, B:Y.164, B:K.168, B:G.197, B:V.199, B:T.201, B:T.201, B:A.202, B:M.203 Water bridges: B:G.21, B:R.41, B:R.41, B:S.66, B:N.91 Salt bridges: B:R.40, B:R.41 NAP.17: 31 residues within 4Å: Chain C: G.15, A.16, S.17, S.18, G.19, I.20, A.39, R.40, R.41, C.63, D.64, V.65, N.91, A.92, G.93, I.94, I.119, I.147, N.148, S.149, Y.164, K.168, P.196, G.197, L.198, V.199, T.201, A.202, M.203, V.205 Ligands: ACT.23 28 PLIP interactions: 28 interactions with chain C Hydrophobic interactions: C:P.196 Hydrogen bonds: C:G.15, C:G.15, C:S.17, C:S.17, C:S.18, C:I.20, C:R.40, C:R.41, C:D.64, C:D.64, C:V.65, C:N.91, C:G.93, C:K.168, C:G.197, C:V.199, C:T.201, C:T.201, C:A.202, C:M.203 Water bridges: C:G.21, C:R.41, C:R.41, C:S.66, C:N.91 Salt bridges: C:R.40, C:R.41 NAP.25: 31 residues within 4Å: Chain D: G.15, A.16, S.17, S.18, G.19, I.20, A.39, R.40, R.41, C.63, D.64, V.65, N.91, A.92, G.93, I.94, I.119, I.147, N.148, S.149, Y.164, K.168, P.196, G.197, L.198, V.199, T.201, A.202, M.203, V.205 Ligands: ACT.31 28 PLIP interactions: 28 interactions with chain D Hydrophobic interactions: D:P.196 Hydrogen bonds: D:G.15, D:G.15, D:S.17, D:S.17, D:S.18, D:I.20, D:R.40, D:R.41, D:D.64, D:D.64, D:V.65, D:N.91, D:G.93, D:K.168, D:G.197, D:V.199, D:T.201, D:T.201, D:A.202, D:M.203 Water bridges: D:G.21, D:R.41, D:R.41, D:S.66, D:N.91 Salt bridges: D:R.40, D:R.41

8 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 7 residues within 4Å: Chain A: I.150, Y.154, F.161, L.198, R.248, L.249 Ligands: ACT.7 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.150, A:F.161 Hydrogen bonds: A:Y.154, A:Y.154, A:L.249 ACT.7: 7 residues within 4Å: Chain A: S.149, I.150, Y.164, P.196, V.205 Ligands: NAP.1, ACT.2 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.150 Hydrogen bonds: A:S.149 ACT.10: 7 residues within 4Å: Chain B: I.150, Y.154, F.161, L.198, R.248, L.249 Ligands: ACT.15 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:I.150, B:F.161 Hydrogen bonds: B:Y.154, B:Y.154, B:L.249 ACT.15: 7 residues within 4Å: Chain B: S.149, I.150, Y.164, P.196, V.205 Ligands: NAP.9, ACT.10 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.150 Hydrogen bonds: B:S.149 ACT.18: 7 residues within 4Å: Chain C: I.150, Y.154, F.161, L.198, R.248, L.249 Ligands: ACT.23 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:I.150, C:F.161 Hydrogen bonds: C:Y.154, C:L.249 Water bridges: C:E.246 ACT.23: 7 residues within 4Å: Chain C: S.149, I.150, Y.164, P.196, V.205 Ligands: NAP.17, ACT.18 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:I.150 Hydrogen bonds: C:S.149, C:Y.164 ACT.26: 7 residues within 4Å: Chain D: I.150, Y.154, F.161, L.198, R.248, L.249 Ligands: ACT.31 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:I.150, D:F.161 Hydrogen bonds: D:Y.154, D:L.249 Water bridges: D:E.246 ACT.31: 7 residues within 4Å: Chain D: S.149, I.150, Y.164, P.196, V.205 Ligands: NAP.25, ACT.26 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:I.150 Hydrogen bonds: D:S.149, D:Y.164

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: T.172, A.176 Chain B: H.153 Chain D: V.155 Ligands: EDO.5 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Water bridges: A:T.172, B:G.152, B:H.153 GOL.11: 5 residues within 4Å: Chain A: H.153 Chain B: T.172, A.176 Chain C: V.155 Ligands: EDO.13 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Water bridges: A:G.152, A:H.153, B:T.172 GOL.19: 5 residues within 4Å: Chain B: V.155 Chain C: T.172, A.176 Chain D: H.153 Ligands: EDO.21 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Water bridges: D:G.152, D:H.153, C:T.172, C:T.172 GOL.27: 5 residues within 4Å: Chain A: V.155 Chain C: H.153 Chain D: T.172, A.176 Ligands: EDO.29 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D Water bridges: C:G.152, C:H.153, D:T.172, D:T.172

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

EDO.4: 7 residues within 4Å: Chain A: S.175, A.176, L.179, V.191, T.192, S.193, N.237 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.191 Water bridges: A:A.176, A:N.237 EDO.5: 6 residues within 4Å: Chain A: H.153, T.172, E.238 Chain B: H.153 Ligands: GOL.3, EDO.13 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:H.153 Water bridges: B:H.153 EDO.6: 3 residues within 4Å: Chain A: A.60, R.61, Q.62 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.62 Water bridges: A:E.46, A:A.60 EDO.12: 7 residues within 4Å: Chain B: S.175, A.176, L.179, V.191, T.192, S.193, N.237 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.191 Water bridges: B:A.176, B:N.237 EDO.13: 6 residues within 4Å: Chain A: H.153 Chain B: H.153, T.172, E.238 Ligands: EDO.5, GOL.11 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:H.153 Hydrogen bonds: B:H.153 EDO.14: 3 residues within 4Å: Chain B: A.60, R.61, Q.62 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.62 Water bridges: B:E.46, B:A.60 EDO.20: 7 residues within 4Å: Chain C: S.175, A.176, L.179, V.191, T.192, S.193, N.237 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:V.191 Water bridges: C:A.176, C:N.237 EDO.21: 6 residues within 4Å: Chain C: H.153, T.172, E.238 Chain D: H.153 Ligands: GOL.19, EDO.29 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:H.153 EDO.22: 3 residues within 4Å: Chain C: A.60, R.61, Q.62 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.62 Water bridges: C:E.46, C:A.60 EDO.28: 7 residues within 4Å: Chain D: S.175, A.176, L.179, V.191, T.192, S.193, N.237 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:V.191 Water bridges: D:A.176, D:N.237 EDO.29: 6 residues within 4Å: Chain C: H.153 Chain D: H.153, T.172, E.238 Ligands: EDO.21, GOL.27 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.153 EDO.30: 3 residues within 4Å: Chain D: A.60, R.61, Q.62 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Q.62 Water bridges: D:E.46, D:A.60

4 x NA: SODIUM ION(Non-functional Binders)

NA.8: 6 residues within 4Å: Chain A: H.143, K.190, V.191, T.192, N.235, I.236 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.191, A:I.236, A:I.236 NA.16: 6 residues within 4Å: Chain B: H.143, K.190, V.191, T.192, N.235, I.236 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.191, B:V.191, B:I.236 NA.24: 6 residues within 4Å: Chain C: H.143, K.190, V.191, T.192, N.235, I.236 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:V.191, C:V.191, C:T.192, C:I.236 NA.32: 6 residues within 4Å: Chain D: H.143, K.190, V.191, T.192, N.235, I.236 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:H.143, D:V.191, D:T.192, D:I.236

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kumar, R. et al., Crystal structure and molecular characterization of NADP + -farnesol dehydrogenase from cotton bollworm, Helicoverpaarmigera. Insect Biochem.Mol.Biol. (2022)

Release Date

2022-07-27

Peptides

Farnesol dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Farnesol dehydrogenase