SMTL ID : 9c5m.2 (1 other biounit)

Trypanosoma cruzi R19T/K20S/C64Y mutant beta-3-HBDH structure in complex with NADH and malonate (P1 space group)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.69 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.3 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.103, A:S.151, A:Q.153, A:Y.164, A:Q.205 Water bridges: A:K.161 Salt bridges: A:K.161 MLI.4: 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.6 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.7: 12 residues within 4Å: Chain C: Q.103, S.151, V.152, Q.153, K.161, Y.164, G.195, Y.196, L.201, V.202, Q.205 Ligands: NAI.10 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.11: 11 residues within 4Å: Chain D: Q.103, S.151, V.152, Q.153, K.161, Y.164, Y.196, L.201, V.202, Q.205 Ligands: NAI.12 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:Q.103, D:S.151, D:Q.153, D:Y.164, D:Q.205 Water bridges: D:K.161 Salt bridges: D:K.161

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

EDO.2: 13 residues within 4Å: Chain A: T.20, N.98, N.99, A.100, G.101, L.122, N.123, S.126, A.127, I.149, K.168, L.171 Ligands: NAI.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.126, A:K.168 Water bridges: A:T.20 EDO.5: 13 residues within 4Å: Chain B: T.20, N.98, N.99, A.100, G.101, L.122, N.123, S.126, A.127, I.149, K.168, L.171 Ligands: NAI.6 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.126, B:K.168 Water bridges: B:T.20 EDO.8: 4 residues within 4Å: Chain C: D.52, S.53, V.56, Y.68 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.53, C:Y.68 Water bridges: C:Y.68 EDO.9: 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: NAI.10 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.98, C:K.168

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

NAI.3: 36 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, 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.1, EDO.2 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:I.26, A:P.194 Hydrogen bonds: A:T.23, 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:K.168, A:V.197, A:V.197, A:T.199, A:T.199, A:L.201 Water bridges: A:G.27, A:R.47, A:K.74, A:K.74, A:N.99 NAI.6: 35 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.4, EDO.5 21 PLIP interactions: 21 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:I.26, B:R.46, B:R.46, B:N.72, B:M.73, B:I.149, B:K.168, B:V.197, B:V.197, B:T.199, B:L.201 Water bridges: B:S.24, B:S.24, B:G.27, B:N.99 NAI.10: 35 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.7, EDO.9 24 PLIP interactions: 24 interactions with chain C Hydrophobic interactions: C:I.26, C:P.194 Hydrogen bonds: C:T.23, C:T.23, C:T.23, C:T.23, C:S.24, C:S.24, C:I.26, C:N.72, C:M.73, C:I.149, 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.24, C:G.27, C:R.46, C:K.74, C:N.99 NAI.12: 34 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.11 25 PLIP interactions: 25 interactions with chain D Hydrophobic interactions: D:I.26, D:P.194 Hydrogen bonds: D:T.23, D:T.23, 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: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:G.27, D:R.47, D:K.74, D:N.99, D:I.149

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
E

B
F

C
G

D
H

Hydroxybutyrate dehydrogenase

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