SMTL ID : 9c5l.1

Trypanosoma cruzi beta-3-HBDH R19T/K20S/C64Y mutant in complex with NADH and malonate (C2 space group)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-tetramer

Ligands

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

MLI.1: 13 residues within 4Å: Chain A: 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: NAI.2 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.103, A:S.151, A:Q.153, A:Y.164, A:Y.164, A:Q.205 Salt bridges: A:K.161 MLI.3: 12 residues within 4Å: Chain B: Q.103, S.151, V.152, Q.153, K.161, Y.164, G.195, Y.196, L.201, V.202, Q.205 Ligands: NAI.4 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.5: 13 residues within 4Å: Chain C: Q.103, S.151, V.152, Q.153, K.161, Y.164, P.194, G.195, Y.196, L.201, V.202, W.267 Ligands: NAI.6 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:Q.103, C:S.151, C:Q.153, C:Y.164 Water bridges: C:K.161 Salt bridges: C:K.161, C:K.161 MLI.7: 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: NAI.9 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:Q.103, D:S.151, D:Q.153, D:Y.164, D:Q.205 Salt bridges: D:K.161

4 x NAI: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE(Non-covalent)

NAI.2: 34 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, 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.1 23 PLIP interactions: 23 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:S.24, A:I.26, A:R.46, A:N.72, A:M.73, A:N.99, A:G.101, A:K.168, A:V.197, A:V.197, A:T.199, A:L.201 Water bridges: A:T.23, A:G.27, A:K.74, A:N.99 NAI.4: 34 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, 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.3 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:I.26, B:P.194 Hydrogen bonds: B:T.23, B:T.23, B:T.23, B:S.24, B:S.24, B:I.26, B:R.46, B:N.72, B:M.73, B:N.99, B:K.168, B:V.197, B:T.199, B:T.199 Water bridges: B:G.27, B:N.99 NAI.6: 34 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, 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.5 21 PLIP interactions: 21 interactions with chain C Hydrophobic interactions: C:I.26, C:P.194 Hydrogen bonds: C:G.21, C:T.23, C:T.23, C:S.24, C:S.24, C:S.24, C:I.26, C:N.72, C:M.73, C:N.99, C:Y.164, C:K.168, C:V.197, C:T.199 Water bridges: C:N.99, C:N.99, C:G.101, C:G.101 pi-Cation interactions: C:R.46 NAI.9: 35 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, 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.7, EDO.8 21 PLIP interactions: 21 interactions with chain D Hydrophobic interactions: D:I.26, D:P.194 Hydrogen bonds: D:T.23, D:T.23, D:T.23, D:S.24, D:S.24, D:I.26, D:R.46, D:M.73, D:N.99, D:Y.164, D:K.168, D:V.197, D:V.197, D:T.199, D:L.201 Water bridges: D:G.27, D:N.99, D:G.101, D:G.101

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

EDO.8: 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: NAI.9 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.98, D:K.168

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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