SMTL ID : 9c5k.1

Trypanosoma cruzi R19T/K20S/C64Y mutant beta-3-HBDH structure in complex with NADPH and malonate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.79 Å

Oligo State

homo-tetramer

Ligands

4 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.1: 38 residues within 4Å: Chain A: G.21, S.22, T.23, S.24, G.25, I.26, G.27, N.44, G.45, R.46, R.47, P.50, A.71, N.72, M.73, K.74, N.99, A.100, G.101, I.102, L.122, I.149, A.150, S.151, V.152, Y.164, K.168, P.194, G.195, Y.196, V.197, T.199, P.200, L.201, V.202 Ligands: EDO.2, MLI.4, SO4.6 30 PLIP interactions: 30 interactions with chain A Hydrophobic interactions: A:I.26, A:P.194 Hydrogen bonds: A:T.23, A:T.23, A:T.23, A:S.24, A:S.24, A:I.26, A:R.46, A:N.72, A:M.73, A:N.99, A:G.101, A:Y.164, A:K.168, A:V.197, A:V.197, A:T.199, A:T.199, A:L.201 Water bridges: A:G.27, A:R.46, A:R.46, A:R.47, A:R.47, A:R.47, A:Y.68, A:N.99 Salt bridges: A:R.46, A:R.47 NDP.7: 36 residues within 4Å: Chain B: G.21, S.22, T.23, S.24, G.25, I.26, G.27, N.44, G.45, R.46, R.47, A.71, N.72, M.73, K.74, N.99, A.100, G.101, I.102, L.122, I.149, A.150, S.151, V.152, Y.164, K.168, P.194, G.195, Y.196, V.197, T.199, P.200, L.201, V.202 Ligands: MLI.10, SO4.12 28 PLIP interactions: 28 interactions with chain B Hydrophobic interactions: B:I.26, B:P.194 Hydrogen bonds: B:G.21, B:T.23, B:T.23, B:T.23, B:T.23, B:S.24, B:S.24, B:I.26, B:R.46, B:M.73, B:A.100, B:Y.164, B:K.168, B:V.197, B:V.197, B:T.199, B:T.199, B:L.201 Water bridges: B:G.27, B:R.46, B:R.46, B:R.46, B:R.47, B:K.74, B:N.99 Salt bridges: B:R.46 NDP.14: 38 residues within 4Å: Chain C: G.21, S.22, T.23, S.24, G.25, I.26, G.27, N.44, G.45, R.46, R.47, A.71, N.72, M.73, K.74, N.99, A.100, G.101, I.102, L.122, N.123, I.149, A.150, S.151, V.152, Y.164, K.168, P.194, G.195, Y.196, V.197, T.199, P.200, L.201, V.202 Ligands: EDO.15, ACT.16, MLI.18 26 PLIP interactions: 26 interactions with chain C Hydrophobic interactions: C:I.26, C:P.194 Hydrogen bonds: C:G.21, C:T.23, C:T.23, C:T.23, C:S.24, C:S.24, C:S.24, C:I.26, C:R.46, C:M.73, C:N.99, C:K.168, C:V.197, C:V.197, C:T.199, C:T.199, C:L.201 Water bridges: C:G.27, C:R.46, C:R.46, C:R.47, C:K.74, C:N.99 Salt bridges: C:R.46 NDP.21: 37 residues within 4Å: Chain D: G.21, S.22, T.23, S.24, G.25, I.26, G.27, N.44, G.45, R.46, R.47, A.71, N.72, M.73, K.74, N.99, A.100, G.101, I.102, L.122, N.123, I.149, A.150, S.151, V.152, Y.164, K.168, P.194, G.195, Y.196, V.197, T.199, P.200, L.201, V.202 Ligands: MLI.22, SO4.24 26 PLIP interactions: 26 interactions with chain D Hydrophobic interactions: D:I.26, D:P.194 Hydrogen bonds: D:T.23, D:T.23, D:S.24, D:S.24, D:I.26, D:R.46, D:N.72, D:M.73, D:A.100, D:G.101, D:K.168, D:V.197, D:V.197, D:T.199, D:T.199, D:L.201 Water bridges: D:T.23, D:G.27, D:R.46, D:R.47, D:R.47, D:K.74, D:N.99 Salt bridges: D:R.46

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

EDO.2: 11 residues within 4Å: Chain A: N.98, N.99, A.100, G.101, L.122, N.123, A.127, I.149, K.168, L.171 Ligands: NDP.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.98, A:K.168 EDO.8: 7 residues within 4Å: Chain B: V.105, K.161, Y.196, Q.205, V.209, F.225, E.228 3 PLIP interactions: 3 interactions with chain B Water bridges: B:K.161, B:K.161, B:Q.205 EDO.9: 5 residues within 4Å: Chain B: E.80, I.83, K.84, E.87, L.133 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.80, B:K.84, B:E.87 EDO.15: 11 residues within 4Å: Chain C: N.98, N.99, A.100, G.101, L.122, N.123, A.127, I.149, K.168, L.171 Ligands: NDP.14 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.98, C:K.168

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

ACT.3: 3 residues within 4Å: Chain A: R.47, Q.48, S.49 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.48, A:S.49 ACT.16: 5 residues within 4Å: Chain C: R.46, R.47, N.72, K.74 Ligands: NDP.14 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:N.72 Water bridges: C:R.46, C:R.46, C:R.46 Salt bridges: C:R.46, C:K.74 ACT.17: 3 residues within 4Å: Chain C: R.47, Q.48, S.49 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:R.47 Hydrogen bonds: C:Q.48, C:S.49

4 x MLI: MALONATE ION(Non-functional Binders)

MLI.4: 11 residues within 4Å: Chain A: Q.103, S.151, Q.153, K.161, Y.164, Y.196, L.201, V.202, Q.205, W.267 Ligands: NDP.1 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Q.103, A:S.151, A:Q.153, A:Y.164, A:Y.164, A:Q.205 Water bridges: A:V.152, A:K.161 Salt bridges: A:K.161 MLI.10: 10 residues within 4Å: Chain B: Q.103, S.151, Q.153, K.161, Y.164, Y.196, L.201, V.202, Q.205 Ligands: NDP.7 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.201 Hydrogen bonds: B:Q.103, B:S.151, B:Q.153, B:Y.164, B:Q.205 Salt bridges: B:K.161 MLI.18: 10 residues within 4Å: Chain C: Q.103, S.151, Q.153, K.161, Y.164, Y.196, L.201, V.202, Q.205 Ligands: NDP.14 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:L.201 Hydrogen bonds: C:Q.103, C:S.151, C:Q.153, C:Y.164, C:Y.164, C:Q.205 Salt bridges: C:K.161 MLI.22: 11 residues within 4Å: Chain D: Q.103, S.151, Q.153, K.161, Y.164, Y.196, L.201, V.202, Q.205, W.267 Ligands: NDP.21 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:L.201 Hydrogen bonds: D:Q.103, D:S.151, D:Q.153, D:Y.164, D:Q.205 Water bridges: D:V.152 Salt bridges: D:K.161

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

SO4.5: 3 residues within 4Å: Chain A: R.65, V.66, R.67 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.67 Salt bridges: A:R.67 SO4.6: 5 residues within 4Å: Chain A: R.46, N.72, K.74, E.118 Ligands: NDP.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.72 Water bridges: A:R.46, A:K.74, A:K.74, A:E.118 Salt bridges: A:R.46, A:K.74 SO4.11: 3 residues within 4Å: Chain B: R.65, V.66, R.67 2 PLIP interactions: 2 interactions with chain B Water bridges: B:V.66 Salt bridges: B:R.67 SO4.12: 5 residues within 4Å: Chain B: R.46, R.47, N.72, K.74 Ligands: NDP.7 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.72 Water bridges: B:R.46, B:K.74, B:E.118, B:E.118 Salt bridges: B:R.46, B:K.74 SO4.13: 3 residues within 4Å: Chain B: R.47, Q.48, S.49 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.48, B:S.49 Water bridges: B:Q.48 SO4.19: 3 residues within 4Å: Chain C: R.65, V.66, R.67 4 PLIP interactions: 4 interactions with chain C Water bridges: C:V.66, C:R.67, C:R.67 Salt bridges: C:R.67 SO4.20: 4 residues within 4Å: Chain C: K.9, R.10, S.13, G.38 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:K.9, C:R.10, C:S.13, C:S.13 Salt bridges: C:R.10 SO4.23: 5 residues within 4Å: Chain D: E.8, K.9, R.10, S.13, G.38 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:K.9, D:R.10, D:S.13, D:S.13 Salt bridges: D:R.10 SO4.24: 6 residues within 4Å: Chain D: R.46, R.47, N.72, K.74, E.118 Ligands: NDP.21 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:R.47, D:N.72 Water bridges: D:R.46, D:R.46 Salt bridges: D:R.46, D:K.74

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hashimoto, H. et al., Trypanosoma cruzi D-3-hydroxybutyrate dehydrogenase (HBDH) is NADP-dependent enzyme. To Be Published

Release Date

2025-08-27

Peptides

Hydroxybutyrate dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Hydroxybutyrate dehydrogenase

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