SMTL ID : 9c5m.1 (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.5 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.6: 13 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, W.267 Ligands: NAI.8 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.201 Hydrogen bonds: B:Q.103, B:S.151, B:Q.153, B:Y.164, B:Y.164, B:Q.205 Salt bridges: B:K.161 MLI.9: 13 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, W.267 Ligands: NAI.11 7 PLIP interactions: 7 interactions with chain C 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.12: 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.14 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:K.161 Salt bridges: D:K.161

6 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: NAI.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.98, A:K.168 EDO.3: 4 residues within 4Å: Chain A: R.67, Y.68, F.85, E.89 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.68, A:Y.68 EDO.4: 4 residues within 4Å: Chain A: D.217, M.218, E.219, A.220 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.217, A:M.218, A:E.219, A:E.219 Water bridges: A:A.220 EDO.7: 5 residues within 4Å: Chain B: Q.48, S.49, D.52, Y.68, A.70 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.52 EDO.10: 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.11 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.98, C:K.168 EDO.13: 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.14 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.98, D:K.168

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

NAI.5: 35 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, EDO.2 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:I.26, A:P.194 Hydrogen bonds: 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: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.47, A:K.74, A:N.99 NAI.8: 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.6 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:I.26, B:P.194 Hydrogen bonds: B:T.23, B:S.24, B:S.24, B:I.26, B:R.46, B:N.72, B:M.73, B:G.101, B:I.149, B:Y.164, B:K.168, B:V.197, B:V.197, B:T.199, B:T.199, B:L.201 Water bridges: B:T.23, B:G.27, B:K.74, B:N.99 NAI.11: 36 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, 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.9, EDO.10 18 PLIP interactions: 18 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:I.26, C:N.72, C:M.73, C:I.149, C:K.168, C:V.197, C:V.197, C:T.199 Water bridges: C:G.27, C:R.46, C:K.74, C:N.99 NAI.14: 36 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, 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.12, EDO.13 23 PLIP interactions: 23 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: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:S.24, D:G.27, D:K.74, D:N.99

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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