SMTL ID : 1u4o.1

Plasmodium falciparum lactate dehydrogenase complexed with 2,6-naphthalenedicarboxylic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-tetramer

Ligands

4 x NDD: 2,6-DICARBOXYNAPHTHALENE(Non-covalent)

NDD.1: 11 residues within 4Å: Chain A: M.13, I.14, V.124, L.153, H.181, S.233, P.234, Y.235, P.238 Ligands: MPD.2, MPD.3 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:I.14, A:I.14, A:V.124, A:Y.235, A:P.238, A:P.238 Hydrogen bonds: A:M.13, A:I.14 Water bridges: A:R.157, A:R.157, A:H.181, A:S.233 Salt bridges: A:H.181 NDD.4: 11 residues within 4Å: Chain B: M.13, I.14, V.124, L.153, H.181, S.233, P.234, Y.235, P.238 Ligands: MPD.5, MPD.6 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:I.14, B:I.14, B:V.124, B:Y.235, B:P.238, B:P.238 Hydrogen bonds: B:M.13, B:I.14 Water bridges: B:R.157, B:R.157, B:H.181, B:S.233 Salt bridges: B:H.181 NDD.7: 11 residues within 4Å: Chain C: M.13, I.14, V.124, L.153, H.181, S.233, P.234, Y.235, P.238 Ligands: MPD.8, MPD.9 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:I.14, C:I.14, C:V.124, C:Y.235, C:P.238, C:P.238 Hydrogen bonds: C:M.13, C:I.14 Water bridges: C:R.157, C:R.157, C:H.181, C:S.233 Salt bridges: C:H.181 NDD.10: 11 residues within 4Å: Chain D: M.13, I.14, V.124, L.153, H.181, S.233, P.234, Y.235, P.238 Ligands: MPD.11, MPD.12 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:I.14, D:I.14, D:V.124, D:Y.235, D:P.238, D:P.238 Hydrogen bonds: D:M.13, D:I.14 Water bridges: D:R.157, D:R.157, D:H.181, D:S.233 Salt bridges: D:H.181

8 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.2: 7 residues within 4Å: Chain A: T.78, T.82, V.124, T.125, N.126 Ligands: NDD.1, MPD.3 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.82 Hydrogen bonds: A:N.126 Water bridges: A:N.126 MPD.3: 5 residues within 4Å: Chain A: R.94, L.225, V.228 Ligands: NDD.1, MPD.2 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.225 Hydrogen bonds: A:R.94 MPD.5: 7 residues within 4Å: Chain B: T.78, T.82, V.124, T.125, N.126 Ligands: NDD.4, MPD.6 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:T.82 Hydrogen bonds: B:N.126 Water bridges: B:N.126 MPD.6: 5 residues within 4Å: Chain B: R.94, L.225, V.228 Ligands: NDD.4, MPD.5 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.225 Hydrogen bonds: B:R.94 MPD.8: 7 residues within 4Å: Chain C: T.78, T.82, V.124, T.125, N.126 Ligands: NDD.7, MPD.9 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:T.82 Hydrogen bonds: C:N.126 Water bridges: C:N.126 MPD.9: 5 residues within 4Å: Chain C: R.94, L.225, V.228 Ligands: NDD.7, MPD.8 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.225 Hydrogen bonds: C:R.94 MPD.11: 7 residues within 4Å: Chain D: T.78, T.82, V.124, T.125, N.126 Ligands: NDD.10, MPD.12 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:T.82 Hydrogen bonds: D:N.126 Water bridges: D:N.126 MPD.12: 5 residues within 4Å: Chain D: R.94, L.225, V.228 Ligands: NDD.10, MPD.11 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:L.225 Hydrogen bonds: D:R.94

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Conners, R. et al., Mapping the binding site for gossypol-like inhibitors of Plasmodium falciparum lactate dehydrogenase. Mol.Biochem.Parasitol. (2005)

Release Date

2005-06-21

Peptides

L-lactate dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

L-lactate dehydrogenase

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