SMTL ID : 5jwa.1

the structure of malaria PfNDH2

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.16 Å

Oligo State

homo-dimer

Ligands

2 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.1: 31 residues within 4Å: Chain A: G.35, S.36, G.37, W.38, G.39, I.57, S.58, P.59, R.60, T.66, P.67, E.104, C.105, A.135, V.136, G.137, V.155, T.199, L.304, G.341, D.342, P.422, T.423, A.424, Q.425, A.427, Y.492 Ligands: MG.2, MG.3, MG.4, MG.5 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:T.199 Hydrogen bonds: A:S.36, A:S.36, A:W.38, A:G.39, A:S.58, A:T.66, A:T.66, A:C.105, A:C.105, A:G.137, A:D.342, A:P.422, A:A.424, A:Q.425, A:Y.492 Water bridges: A:R.60, A:R.60, A:K.156, A:K.156, A:T.199, A:Q.425, A:A.427 FAD.14: 32 residues within 4Å: Chain B: G.35, S.36, G.37, W.38, G.39, I.57, S.58, P.59, R.60, T.66, P.67, E.104, C.105, A.135, V.136, G.137, V.155, K.156, T.199, L.304, G.341, D.342, P.422, T.423, A.424, Q.425, A.427, Y.492 Ligands: MG.15, MG.16, MG.17, MG.18 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:T.199 Hydrogen bonds: B:S.36, B:S.36, B:W.38, B:G.39, B:S.58, B:T.66, B:C.105, B:C.105, B:G.137, B:D.342, B:P.422, B:A.424, B:Q.425 Water bridges: B:R.60, B:R.60, B:E.104, B:K.156, B:K.156, B:A.427 Salt bridges: B:K.156

8 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 8 residues within 4Å: Chain A: A.135, V.136, G.137, I.340, G.341, D.342, C.343 Ligands: FAD.1 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:I.340, FAD.1 MG.3: 8 residues within 4Å: Chain A: G.35, S.36, G.37, W.38, G.39, G.40, A.135 Ligands: FAD.1 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:A.135, FAD.1 MG.4: 7 residues within 4Å: Chain A: G.37, W.38, R.60, F.63, T.64, T.66 Ligands: FAD.1 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.64, H2O.3 MG.5: 5 residues within 4Å: Chain A: G.137, A.138, K.156, D.342 Ligands: FAD.1 No protein-ligand interaction detected (PLIP) MG.15: 8 residues within 4Å: Chain B: A.135, V.136, G.137, I.340, G.341, D.342, C.343 Ligands: FAD.14 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:I.340, FAD.14 MG.16: 8 residues within 4Å: Chain B: G.35, S.36, G.37, W.38, G.39, G.40, A.135 Ligands: FAD.14 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:A.135 MG.17: 6 residues within 4Å: Chain B: G.37, W.38, R.60, T.64, T.66 Ligands: FAD.14 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:T.64, H2O.10 MG.18: 5 residues within 4Å: Chain B: G.137, A.138, K.156, D.342 Ligands: FAD.14 No protein-ligand interaction detected (PLIP)

6 x TRT: FRAGMENT OF TRITON X-100(Non-covalent)

TRT.6: 7 residues within 4Å: Chain A: Y.515 Chain B: I.493, W.499, R.502, F.503, F.506 Ligands: TRT.21 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:I.493, B:W.499, B:F.503, B:F.503, B:F.506, B:F.506, B:F.506 TRT.7: 4 residues within 4Å: Chain A: I.493, Q.494, R.502 Ligands: TRT.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.502, A:R.502 TRT.8: 8 residues within 4Å: Chain A: K.489, V.490, I.493, F.506, F.509, K.513 Ligands: TRT.7, TRT.19 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.493, A:F.506, A:K.513 Hydrogen bonds: A:K.489 TRT.19: 6 residues within 4Å: Chain A: I.493, W.499, F.503, F.506 Chain B: Y.515 Ligands: TRT.8 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.493, A:W.499, A:F.503, A:F.503, A:F.506, A:F.506, A:F.506 Hydrogen bonds: B:Y.515 TRT.20: 8 residues within 4Å: Chain B: K.489, I.493, F.505, F.506, F.509, I.510, K.513 Ligands: TRT.21 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:K.489, B:K.489, B:I.493, B:I.493, B:F.505, B:F.506, B:F.509, B:K.513 TRT.21: 4 residues within 4Å: Chain B: Q.494, R.502 Ligands: TRT.6, TRT.20 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.502, B:R.502

12 x ACT: ACETATE ION(Non-functional Binders)

ACT.9: 3 residues within 4Å: Chain A: V.469, S.485, W.488 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.469, A:W.488 ACT.10: 4 residues within 4Å: Chain A: D.209, K.213, H.467, R.517 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:K.213, A:H.467, A:R.517 ACT.11: 3 residues within 4Å: Chain A: N.212, L.256, N.257 1 PLIP interactions: 1 interactions with chain A Water bridges: A:I.228 ACT.12: 5 residues within 4Å: Chain A: N.218, Y.219, K.220, D.221 Chain B: R.87 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:R.87, A:D.221, A:I.222 Water bridges: B:N.99, B:N.99, A:N.218 Hydrophobic interactions: A:K.220 ACT.13: 6 residues within 4Å: Chain A: G.75, T.76, D.508, K.511, T.512, P.518 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.511 Salt bridges: A:K.511 ACT.22: 4 residues within 4Å: Chain B: N.212, I.226, L.256, N.257 2 PLIP interactions: 2 interactions with chain B Water bridges: B:I.228, B:I.228 ACT.23: 4 residues within 4Å: Chain B: D.209, K.213, H.467, R.517 3 PLIP interactions: 3 interactions with chain B Salt bridges: B:K.213, B:H.467, B:R.517 ACT.24: 2 residues within 4Å: Chain B: S.485, W.488 No protein-ligand interaction detected (PLIP) ACT.25: 3 residues within 4Å: Chain A: R.165, P.518 Chain B: N.80 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.518 Salt bridges: A:R.165 ACT.26: 4 residues within 4Å: Chain B: K.150, Y.151, A.152, Y.153 1 PLIP interactions: 1 interactions with chain B Water bridges: B:A.152 ACT.27: 7 residues within 4Å: Chain B: F.143, I.145, V.194, Y.265, V.266, W.295, S.297 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.145, B:Y.265 Hydrogen bonds: B:V.266, B:S.297 ACT.28: 3 residues within 4Å: Chain B: K.381, F.448, N.449 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.326

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, Y. et al., Target Elucidation by Cocrystal Structures of NADH-Ubiquinone Oxidoreductase of Plasmodium falciparum (PfNDH2) with Small Molecule To Eliminate Drug-Resistant Malaria. J. Med. Chem. (2017)

Release Date

2017-03-22

Peptides

NADH dehydrogenase, putative: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
H

NADH dehydrogenase, putative

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