- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.05 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)
- 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: 7 residues within 4Å:- Chain A: G.35, 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: 6 residues within 4Å:- Chain A: G.37, W.38, R.60, F.63, T.64
- Ligands: FAD.1
2 PLIP interactions:1 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:T.64, H2O.5
MG.5: 4 residues within 4Å:- Chain A: G.137, A.138, K.156
- Ligands: FAD.1
No protein-ligand interaction detected (PLIP)MG.13: 8 residues within 4Å:- Chain B: A.135, V.136, G.137, I.340, G.341, D.342, C.343
- Ligands: FAD.12
2 PLIP interactions:1 interactions with chain B, 1 Ligand-Ligand interactions- Metal complexes: B:I.340, FAD.12
MG.14: 8 residues within 4Å:- Chain B: G.35, S.36, G.37, W.38, G.39, G.40, A.135
- Ligands: FAD.12
2 PLIP interactions:1 interactions with chain B, 1 Ligand-Ligand interactions- Metal complexes: B:A.135, FAD.12
MG.15: 7 residues within 4Å:- Chain B: G.37, W.38, R.60, F.63, T.64, T.66
- Ligands: FAD.12
2 PLIP interactions:1 interactions with chain B, 1 Ligand-Water interactions- Metal complexes: B:T.64, H2O.13
MG.16: 5 residues within 4Å:- Chain B: G.137, A.138, K.156, D.342
- Ligands: FAD.12
No protein-ligand interaction detected (PLIP)- 6 x TRT: FRAGMENT OF TRITON X-100(Non-covalent)
TRT.6: 6 residues within 4Å:- Chain A: I.493, Q.494, L.497, W.499, R.502
- Ligands: TRT.18
4 PLIP interactions:4 interactions with chain A- Hydrophobic interactions: A:I.493, A:Q.494
- Hydrogen bonds: A:R.502, A:R.502
TRT.7: 5 residues within 4Å:- Chain A: Y.515
- Chain B: I.493, W.499, F.503, F.506
5 PLIP interactions:5 interactions with chain B- Hydrophobic interactions: B:I.493, B:W.499, B:F.503, B:F.503, B:F.506
TRT.8: 13 residues within 4Å:- Chain A: W.38, A.424, Q.425, K.428, K.458, G.459, L.461, V.490, V.491, Y.492, Q.494, L.495
- Ligands: FAD.1
5 PLIP interactions:5 interactions with chain A- Hydrophobic interactions: A:V.490, A:V.491, A:Q.494, A:L.495
- Hydrogen bonds: A:Q.425
TRT.17: 5 residues within 4Å:- Chain B: I.493, Q.494, L.497, W.499, R.502
4 PLIP interactions:4 interactions with chain B- Hydrophobic interactions: B:I.493, B:Q.494
- Hydrogen bonds: B:R.502, B:R.502
TRT.18: 6 residues within 4Å:- Chain A: W.499, R.502, F.503, F.506
- Chain B: Y.515
- Ligands: TRT.6
6 PLIP interactions:5 interactions with chain A, 1 interactions with chain B- Hydrophobic interactions: A:F.503, A:F.506, A:F.506, A:F.506
- Water bridges: A:W.499
- Hydrogen bonds: B:Y.515
TRT.19: 11 residues within 4Å:- Chain B: W.38, Q.425, K.428, K.458, G.459, V.490, V.491, Y.492, Q.494, L.495
- Ligands: FAD.12
8 PLIP interactions:8 interactions with chain B- Hydrophobic interactions: B:V.490, B:V.491, B:V.491, B:L.495
- Water bridges: B:Q.425, B:Q.425, B:Q.425, B:Q.425
- 4 x 4W0: 5-fluoro-3-methyl-2-{4-[4-(trifluoromethoxy)benzyl]phenyl}quinolin-4(1H)-one(Non-covalent)
4W0.9: 15 residues within 4Å:- Chain A: Y.62, V.79, N.80, I.158, D.159, L.162
- Chain B: L.72, G.75, L.77, S.78, L.162, R.165, P.518, I.520, K.521
12 PLIP interactions:5 interactions with chain B, 7 interactions with chain A- Hydrophobic interactions: B:L.72, B:L.162, B:P.518, B:I.520, A:V.79, A:V.79, A:I.158, A:D.159, A:L.162
- Halogen bonds: B:K.521
- Hydrogen bonds: A:N.80
- Water bridges: A:D.159
4W0.10: 15 residues within 4Å:- Chain A: L.72, G.75, L.77, S.78, L.162, R.165, P.518, I.520, K.521
- Chain B: Y.62, V.79, N.80, I.158, D.159, L.162
13 PLIP interactions:7 interactions with chain B, 6 interactions with chain A- Hydrophobic interactions: B:V.79, B:V.79, B:I.158, B:D.159, B:L.162, A:L.72, A:L.162, A:P.518, A:I.520, A:I.520
- Hydrogen bonds: B:Y.62, B:N.80
- Halogen bonds: A:K.521
4W0.11: 11 residues within 4Å:- Chain A: E.206, D.209, N.212, K.213, Y.463, N.466, H.467, S.485, W.488, K.489, R.517
12 PLIP interactions:12 interactions with chain A- Hydrophobic interactions: A:D.209, A:N.212, A:K.213, A:K.213
- Hydrogen bonds: A:D.209, A:S.485, A:K.489
- Water bridges: A:T.76
- pi-Stacking: A:Y.463, A:W.488
- Halogen bonds: A:N.466, A:S.485
4W0.20: 11 residues within 4Å:- Chain B: E.206, D.209, N.212, K.213, Y.463, N.466, H.467, S.485, W.488, K.489, R.517
11 PLIP interactions:11 interactions with chain B- Hydrophobic interactions: B:D.209, B:N.212, B:K.213
- Hydrogen bonds: B:D.209, B:D.209, B:S.485, B:K.489
- Water bridges: B:Y.463
- pi-Stacking: B:Y.463, B:W.488
- Halogen bonds: B:S.485
- 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
AB
H
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.05 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)
- 8 x MG: MAGNESIUM ION(Non-covalent)
- 6 x TRT: FRAGMENT OF TRITON X-100(Non-covalent)
- 4 x 4W0: 5-fluoro-3-methyl-2-{4-[4-(trifluoromethoxy)benzyl]phenyl}quinolin-4(1H)-one(Non-covalent)
- 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
AB
H