SMTL ID : 9c5h.1

Trypanosoma cruzi beta-3-HBDH structure in complex with NADPH and malonate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.59 Å

Oligo State

homo-tetramer

Ligands

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

NDP.1: 36 residues within 4Å: Chain A: G.21, S.22, R.23, K.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.2 31 PLIP interactions: 31 interactions with chain A Hydrophobic interactions: A:I.26, A:P.194 Hydrogen bonds: A:G.21, A:R.23, A:K.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:L.201 Water bridges: A:S.22, A:R.23, A:R.23, A:K.24, A:K.24, A:K.24, A:G.27, A:G.27, A:R.47, A:K.74 Salt bridges: A:R.23, A:K.24, A:R.46 pi-Cation interactions: A:R.46 NDP.9: 37 residues within 4Å: Chain B: G.21, S.22, R.23, K.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.6, MLI.10 28 PLIP interactions: 28 interactions with chain B Hydrophobic interactions: B:I.26, B:P.194 Hydrogen bonds: B:G.21, B:R.23, B:K.24, B:I.26, B:R.46, B:M.73, B:N.99, B:G.101, B:Y.164, B:K.168, B:V.197, B:V.197, B:T.199, B:T.199, B:L.201 Water bridges: B:S.22, B:R.23, B:R.23, B:K.24, B:K.24, B:G.27, B:R.47, B:N.99 Salt bridges: B:R.23, B:K.24, B:R.46 NDP.15: 37 residues within 4Å: Chain C: G.21, S.22, R.23, K.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.11, MLI.16 27 PLIP interactions: 27 interactions with chain C Hydrophobic interactions: C:I.26, C:P.194 Hydrogen bonds: C:G.21, C:R.23, C:K.24, C:K.24, C:I.26, C:R.46, C:M.73, C:N.99, C:G.101, C:Y.164, C:K.168, C:V.197, C:V.197, C:T.199, C:T.199, C:L.201 Water bridges: C:S.22, C:R.23, C:K.24, C:G.27, C:R.46, C:R.47 Salt bridges: C:R.23, C:K.24, C:R.46 NDP.18: 37 residues within 4Å: Chain D: G.21, S.22, R.23, K.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.17, MLI.19 29 PLIP interactions: 29 interactions with chain D Hydrophobic interactions: D:I.26, D:P.194 Hydrogen bonds: D:G.21, D:R.23, D:K.24, D:I.26, D:R.46, D:M.73, D:A.100, D:G.101, D:Y.164, D:K.168, D:V.197, D:V.197, D:T.199, D:T.199, D:L.201 Water bridges: D:S.22, D:R.23, D:R.23, D:K.24, D:K.24, D:G.27, D:R.47, D:K.74, D:N.99 Salt bridges: D:R.23, D:K.24, D:R.46

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

MLI.2: 12 residues within 4Å: Chain A: Q.103, S.151, V.152, Q.153, K.161, Y.164, Y.196, L.201, V.202, Q.205, W.267 Ligands: NDP.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.201 Hydrogen bonds: A:Q.103, A:S.151, A:Q.153, A:Y.164, A:Q.205 Salt bridges: A:K.161 MLI.10: 11 residues within 4Å: Chain B: Q.103, S.151, V.152, Q.153, K.161, Y.164, Y.196, L.201, V.202, Q.205 Ligands: NDP.9 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.201 Hydrogen bonds: B:Q.103, B:S.151, B:Q.153, B:Q.205 Salt bridges: B:K.161 MLI.16: 11 residues within 4Å: Chain C: Q.103, S.151, V.152, Q.153, K.161, Y.164, Y.196, L.201, V.202, Q.205 Ligands: NDP.15 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:L.201 Hydrogen bonds: C:Q.103, C:S.151, C:Q.153, C:Y.164, C:Q.205 Salt bridges: C:K.161 MLI.19: 13 residues within 4Å: Chain D: Q.103, S.151, V.152, Q.153, K.161, Y.164, G.195, Y.196, L.201, V.202, Q.205, W.267 Ligands: NDP.18 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:L.201 Hydrogen bonds: D:Q.103, D:S.151, D:Q.153, D:Q.205 Salt bridges: D:K.161

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

EDO.3: 10 residues within 4Å: Chain A: L.155, V.156, V.268, A.269, Q.270 Chain C: L.155, V.156, V.268, A.269, Q.270 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:V.268, C:Q.270, A:V.268, A:Q.270 EDO.4: 7 residues within 4Å: Chain B: Q.48, S.49, P.50, E.51, D.52, S.53, A.54 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.48, B:D.52, B:S.53, B:S.53 Water bridges: B:A.54 EDO.5: 10 residues within 4Å: Chain B: L.155, V.156, V.268, A.269, Q.270 Chain D: L.155, V.156, V.268, A.269, Q.270 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:V.268, D:V.268 EDO.6: 11 residues within 4Å: Chain B: N.98, N.99, A.100, G.101, L.122, N.123, A.127, I.149, K.168, L.171 Ligands: NDP.9 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.98, B:K.168 EDO.7: 7 residues within 4Å: Chain B: F.69, A.70, A.71, N.72, A.77, Q.78, A.81 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.70 EDO.8: 7 residues within 4Å: Chain B: E.109, T.110, F.111, P.112, S.113 Chain C: R.76, Q.132 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:E.109, C:R.76, C:Q.132 Water bridges: B:S.113 EDO.11: 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.15 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.98, C:K.168 EDO.12: 3 residues within 4Å: Chain C: T.184, T.185, G.186 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.184 EDO.13: 5 residues within 4Å: Chain C: E.80, I.83, K.84, E.87, L.133 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.80, C:E.80, C:K.84, C:E.87 EDO.17: 11 residues within 4Å: Chain D: N.98, N.99, A.100, G.101, L.122, N.123, A.127, I.149, K.168, L.171 Ligands: NDP.18 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.98, D:K.168

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

PEG.14: 6 residues within 4Å: Chain C: V.56, A.60, T.64, R.65, V.66, R.67 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:V.66, C:R.67, C:R.67 Water bridges: C:R.65

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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