SMTL ID : 3w88.1

Structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with SH-1-200

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-dimer

Ligands

2 x W88: 5-[4-(6-carboxynaphthalen-2-yl)butyl]-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid(Non-covalent)

W88.1: 16 residues within 4Å: Chain A: K.45, N.55, N.69, S.70, M.71, G.72, L.73, P.74, N.129, C.132, P.133, N.196, S.197, K.216 Ligands: GOL.5, FMN.17 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:L.73, A:P.133, A:K.216 Hydrogen bonds: A:N.55, A:N.69, A:N.69, A:M.71, A:G.72, A:L.73, A:N.129, A:N.196, A:N.196, A:S.197 Salt bridges: A:K.45 W88.43: 16 residues within 4Å: Chain B: K.45, R.52, N.69, M.71, G.72, L.73, P.74, L.103, N.129, P.133, N.196, S.197 Ligands: GOL.44, FMN.57, EDO.71, PEG.75 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:L.103, B:L.103, B:P.133 Hydrogen bonds: B:N.69, B:N.69, B:N.69, B:M.71, B:G.72, B:L.73, B:N.129, B:N.196, B:N.196, B:S.197 Salt bridges: B:K.45, B:R.52 pi-Cation interactions: B:R.52

24 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: C.33, A.36, S.37, P.281 Ligand excluded by PLIP GOL.3: 7 residues within 4Å: Chain A: I.173, R.240, R.241 Chain B: K.216, Q.217, F.219 Ligands: EDO.29 Ligand excluded by PLIP GOL.4: 7 residues within 4Å: Chain A: K.216, Q.217, F.219 Chain B: I.173, R.240, R.241 Ligands: GOL.7 Ligand excluded by PLIP GOL.5: 8 residues within 4Å: Chain A: S.131, P.168, P.169, N.196, S.197, G.199, G.221 Ligands: W88.1 Ligand excluded by PLIP GOL.6: 6 residues within 4Å: Chain A: F.63, V.203, I.204, D.205 Ligands: EDO.34, NCO.42 Ligand excluded by PLIP GOL.7: 3 residues within 4Å: Chain A: Q.217 Chain B: R.240 Ligands: GOL.4 Ligand excluded by PLIP GOL.8: 2 residues within 4Å: Chain A: E.279, R.286 Ligand excluded by PLIP GOL.9: 4 residues within 4Å: Chain A: Y.60, M.71, Q.277 Ligands: CAC.15 Ligand excluded by PLIP GOL.10: 8 residues within 4Å: Chain A: V.12, A.14, Y.91, S.92, K.93, K.94, P.95 Ligands: EDO.23 Ligand excluded by PLIP GOL.11: 3 residues within 4Å: Chain A: P.243, K.245 Ligands: GOL.13 Ligand excluded by PLIP GOL.12: 3 residues within 4Å: Chain A: P.243, D.244 Ligands: EDO.35 Ligand excluded by PLIP GOL.13: 4 residues within 4Å: Chain A: Y.239, R.240, P.243 Ligands: GOL.11 Ligand excluded by PLIP GOL.14: 6 residues within 4Å: Chain A: D.53, G.54, N.55, P.56, E.57, R.59 Ligand excluded by PLIP GOL.44: 7 residues within 4Å: Chain B: S.131, Q.140, N.196, S.197, G.199, G.221 Ligands: W88.43 Ligand excluded by PLIP GOL.45: 5 residues within 4Å: Chain B: F.63, V.203, I.204, D.205 Ligands: PEG.73 Ligand excluded by PLIP GOL.46: 4 residues within 4Å: Chain B: Y.60, M.71, Q.277 Ligands: CAC.55 Ligand excluded by PLIP GOL.47: 5 residues within 4Å: Chain B: L.6, N.7, E.304, R.307 Ligands: GOL.48 Ligand excluded by PLIP GOL.48: 7 residues within 4Å: Chain B: P.243, D.244, K.245, L.246 Ligands: GOL.47, GOL.50, CAC.56 Ligand excluded by PLIP GOL.49: 4 residues within 4Å: Chain B: V.12, Y.91, S.92, P.95 Ligand excluded by PLIP GOL.50: 5 residues within 4Å: Chain B: Y.239, R.240, P.243 Ligands: GOL.48, CAC.56 Ligand excluded by PLIP GOL.51: 2 residues within 4Å: Chain B: A.50, P.51 Ligand excluded by PLIP GOL.52: 6 residues within 4Å: Chain A: I.313 Chain B: D.205, S.208, S.210, V.211, V.212 Ligand excluded by PLIP GOL.53: 2 residues within 4Å: Chain B: D.177, A.181 Ligand excluded by PLIP GOL.54: 6 residues within 4Å: Chain B: P.64, K.225, Y.254 Ligands: EDO.59, EDO.60, EDO.72 Ligand excluded by PLIP

4 x CAC: CACODYLATE ION(Non-covalent)

CAC.15: 5 residues within 4Å: Chain A: L.24, S.26, T.27, D.30 Ligands: GOL.9 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.30 Water bridges: A:L.24, A:S.26, A:S.26, A:D.30 CAC.16: 3 residues within 4Å: Chain A: K.298, Y.300 Ligands: EDO.27 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.298 CAC.55: 4 residues within 4Å: Chain B: S.26, T.27, D.30 Ligands: GOL.46 5 PLIP interactions: 5 interactions with chain B Water bridges: B:L.24, B:S.26, B:S.26, B:S.26, B:T.27 CAC.56: 3 residues within 4Å: Chain B: P.243 Ligands: GOL.48, GOL.50 No protein-ligand interaction detected (PLIP)

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.17: 23 residues within 4Å: Chain A: A.20, A.21, G.22, K.45, S.46, Y.60, N.69, M.71, N.129, K.166, V.195, N.196, S.197, G.223, G.224, I.227, C.250, G.251, G.252, V.272, G.273, T.274 Ligands: W88.1 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:Y.60, A:Y.60 Hydrogen bonds: A:A.21, A:S.46, A:S.46, A:S.46, A:K.166, A:K.166, A:N.196, A:G.224, A:G.252, A:G.273, A:T.274 Water bridges: A:A.21, A:S.99, A:G.251, A:G.251, A:V.253, A:V.253 FMN.57: 23 residues within 4Å: Chain B: A.20, A.21, G.22, K.45, S.46, Y.60, N.69, M.71, N.129, K.166, V.195, N.196, S.197, G.223, G.224, I.227, C.250, G.251, G.252, V.272, G.273, T.274 Ligands: W88.43 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:Y.60, B:Y.60 Hydrogen bonds: B:A.21, B:S.46, B:S.46, B:S.46, B:K.166, B:K.166, B:N.196, B:G.224, B:G.252, B:G.273, B:T.274 Water bridges: B:A.21, B:S.99, B:G.251, B:G.251, B:V.253, B:V.253

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

EDO.18: 5 residues within 4Å: Chain A: R.240, G.308, R.309, V.310, T.312 Ligand excluded by PLIP EDO.19: 3 residues within 4Å: Chain A: Q.120, E.121, G.123 Ligand excluded by PLIP EDO.20: 3 residues within 4Å: Chain A: P.51, R.52, D.53 Ligand excluded by PLIP EDO.21: 3 residues within 4Å: Chain A: F.63, P.64, E.278 Ligand excluded by PLIP EDO.22: 3 residues within 4Å: Chain A: G.299, R.301, E.305 Ligand excluded by PLIP EDO.23: 8 residues within 4Å: Chain A: A.14, S.37, S.38, S.39, G.40, K.93, K.94 Ligands: GOL.10 Ligand excluded by PLIP EDO.24: 5 residues within 4Å: Chain A: E.257, R.297, K.298 Chain B: A.206, E.207 Ligand excluded by PLIP EDO.25: 4 residues within 4Å: Chain A: L.65, K.225 Chain B: L.65 Ligands: EDO.72 Ligand excluded by PLIP EDO.26: 4 residues within 4Å: Chain A: E.304, E.305, R.309 Ligands: EDO.27 Ligand excluded by PLIP EDO.27: 3 residues within 4Å: Chain A: Y.300 Ligands: CAC.16, EDO.26 Ligand excluded by PLIP EDO.28: 4 residues within 4Å: Chain A: S.49, A.50, P.51, D.79 Ligand excluded by PLIP EDO.29: 2 residues within 4Å: Chain A: I.173 Ligands: GOL.3 Ligand excluded by PLIP EDO.30: 6 residues within 4Å: Chain A: C.132, P.133, V.135, K.138, P.139 Ligands: EDO.31 Ligand excluded by PLIP EDO.31: 5 residues within 4Å: Chain A: L.103, S.104, V.105, Y.151 Ligands: EDO.30 Ligand excluded by PLIP EDO.32: 4 residues within 4Å: Chain A: S.86, D.87, H.89, K.122 Ligand excluded by PLIP EDO.33: 5 residues within 4Å: Chain A: N.7, L.8, L.9, D.10, H.11 Ligand excluded by PLIP EDO.34: 6 residues within 4Å: Chain A: M.61, F.63, D.205, V.212 Ligands: GOL.6, NCO.42 Ligand excluded by PLIP EDO.35: 7 residues within 4Å: Chain A: N.184, E.185, F.186, P.187, D.244, K.245 Ligands: GOL.12 Ligand excluded by PLIP EDO.58: 4 residues within 4Å: Chain B: S.49, G.77, F.78, D.79 Ligand excluded by PLIP EDO.59: 5 residues within 4Å: Chain B: F.63, P.64, E.278 Ligands: GOL.54, PEG.73 Ligand excluded by PLIP EDO.60: 7 residues within 4Å: Chain B: Y.254, A.275, E.278, E.279, I.283, R.286 Ligands: GOL.54 Ligand excluded by PLIP EDO.61: 4 residues within 4Å: Chain A: L.65 Chain B: L.65, K.225 Ligands: EDO.72 Ligand excluded by PLIP EDO.62: 1 residues within 4Å: Chain B: E.57 Ligand excluded by PLIP EDO.63: 4 residues within 4Å: Chain B: S.86, D.87, H.89, K.122 Ligand excluded by PLIP EDO.64: 3 residues within 4Å: Chain B: P.56, K.214, P.215 Ligand excluded by PLIP EDO.65: 5 residues within 4Å: Chain B: A.119, Q.120, E.121, K.122, G.123 Ligand excluded by PLIP EDO.66: 8 residues within 4Å: Chain B: A.14, N.15, S.37, S.38, S.39, G.40, K.93, K.94 Ligand excluded by PLIP EDO.67: 5 residues within 4Å: Chain B: L.9, D.10, L.125, P.162, K.190 Ligand excluded by PLIP EDO.68: 5 residues within 4Å: Chain A: A.206, E.207 Chain B: E.257, R.297, K.298 Ligand excluded by PLIP EDO.69: 5 residues within 4Å: Chain B: C.3, L.4, E.288, L.292 Ligands: EDO.70 Ligand excluded by PLIP EDO.70: 3 residues within 4Å: Chain B: M.2, L.292 Ligands: EDO.69 Ligand excluded by PLIP EDO.71: 5 residues within 4Å: Chain B: R.52, G.54, N.55, G.72 Ligands: W88.43 Ligand excluded by PLIP EDO.72: 5 residues within 4Å: Chain B: P.64, L.65 Ligands: EDO.25, GOL.54, EDO.61 Ligand excluded by PLIP

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

PEG.36: 11 residues within 4Å: Chain A: Y.143, P.169, Y.170, F.171, D.172, H.175 Chain B: Y.143, Y.170, F.171, D.172, H.175 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:F.171, A:D.172, B:F.171, B:D.172 PEG.37: 5 residues within 4Å: Chain A: C.3, L.4, K.5, A.14, E.288 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.4, A:E.288 PEG.38: 7 residues within 4Å: Chain A: Q.153, S.156, L.157, G.160, L.188 Ligands: PEG.39, PEG.40 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.157 Water bridges: A:Q.153, A:S.156 PEG.39: 7 residues within 4Å: Chain A: R.149, Q.153, E.185, F.186, P.187 Ligands: PEG.38, PEG.40 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.185, A:E.185 PEG.40: 4 residues within 4Å: Chain A: P.187, L.188 Ligands: PEG.38, PEG.39 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.156 PEG.73: 4 residues within 4Å: Chain B: F.63, P.64 Ligands: GOL.45, EDO.59 No protein-ligand interaction detected (PLIP) PEG.74: 4 residues within 4Å: Chain B: E.106, V.109, A.110, R.113 No protein-ligand interaction detected (PLIP) PEG.75: 6 residues within 4Å: Chain B: N.55, S.70, M.71, G.72, K.216 Ligands: W88.43 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.55, B:G.72 Water bridges: B:N.69, B:K.216

2 x NCO: COBALT HEXAMMINE(III)(Non-covalent)

NCO.41: 4 residues within 4Å: Chain A: Q.277, E.278, E.279, G.280 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.277, A:Q.277, A:E.278, A:E.278 NCO.42: 4 residues within 4Å: Chain A: D.205, E.207 Ligands: GOL.6, EDO.34 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.205, A:D.205 Water bridges: A:E.207, A:S.208

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Inaoka, D.K. et al., Structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with SH-1-200. To be Published

Release Date

2014-03-12

Peptides

Dihydroorotate dehydrogenase (fumarate): AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dihydroorotate dehydrogenase (fumarate)

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