SMTL ID : 5jwb.1

Structure of NDH2 from plasmodium falciparum in complex with NADH

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-dimer

Ligands

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

FAD.1: 34 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, L.69, 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.2, MG.3, MG.4, MG.5, NAD.8 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:L.69, A:K.156, 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:A.427 FAD.16: 33 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, L.69, 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.17, MG.18, MG.19, MG.20, NAD.21 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:L.69 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

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, S.36, G.37, 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: 5 residues within 4Å: Chain A: G.37, R.60, T.64, T.66 Ligands: FAD.1 No protein-ligand interaction detected (PLIP) 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.17: 8 residues within 4Å: Chain B: A.135, V.136, G.137, I.340, G.341, D.342, C.343 Ligands: FAD.16 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:I.340, FAD.16 MG.18: 7 residues within 4Å: Chain B: G.35, G.37, W.38, G.39, G.40, A.135 Ligands: FAD.16 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:A.135, FAD.16 MG.19: 5 residues within 4Å: Chain B: G.37, W.38, R.60, T.64 Ligands: FAD.16 No protein-ligand interaction detected (PLIP) MG.20: 5 residues within 4Å: Chain B: G.137, A.138, K.156, D.342 Ligands: FAD.16 No protein-ligand interaction detected (PLIP)

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

TRT.6: 7 residues within 4Å: Chain A: K.489, I.493, F.506, F.509, I.510, K.513 Ligands: TRT.7 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:K.489, A:I.493, A:F.506, A:F.509 Hydrogen bonds: A:K.489 TRT.7: 6 residues within 4Å: Chain A: V.490, I.493, Q.494, L.497, R.502 Ligands: TRT.6 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.490, A:I.493, A:Q.494 Hydrogen bonds: A:R.502, A:R.502 TRT.9: 6 residues within 4Å: Chain A: Y.515 Chain B: I.493, W.499, R.502, 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.506, B:F.506 TRT.15: 5 residues within 4Å: Chain A: I.493, W.499, F.503, F.506 Chain B: Y.515 6 PLIP interactions: 1 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:Y.515 Hydrophobic interactions: A:I.493, A:W.499, A:F.503, A:F.506, A:F.506 TRT.22: 7 residues within 4Å: Chain B: K.489, I.493, F.506, F.509, I.510, K.513 Ligands: TRT.23 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:K.489, B:I.493, B:F.506, B:F.509, B:K.513 TRT.23: 5 residues within 4Å: Chain B: I.493, Q.494, W.499, R.502 Ligands: TRT.22 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:I.493, B:Q.494, B:W.499 Hydrogen bonds: B:R.502, B:R.502

2 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.8: 23 residues within 4Å: Chain A: F.143, V.194, G.195, G.196, G.197, P.198, T.199, E.202, I.231, E.232, G.233, P.239, Y.264, Y.265, V.266, A.296, S.297, G.298, P.422, T.423, S.460, L.461 Ligands: FAD.1 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:P.198 Hydrogen bonds: A:G.196, A:G.197, A:T.199, A:T.199, A:E.202, A:G.233, A:V.266, A:V.266, A:A.296, A:L.461 pi-Stacking: A:Y.265 NAD.21: 22 residues within 4Å: Chain B: F.143, V.194, G.195, G.196, G.197, P.198, T.199, E.202, I.231, E.232, G.233, P.239, Y.264, Y.265, V.266, A.296, S.297, G.298, P.422, T.423, L.461 Ligands: FAD.16 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:P.198 Hydrogen bonds: B:G.196, B:G.197, B:T.199, B:T.199, B:G.233, B:V.266, B:V.266, B:L.461

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

ACT.10: 3 residues within 4Å: Chain A: N.212, L.256, N.257 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:N.257 Hydrogen bonds: A:N.212, A:I.226 ACT.11: 5 residues within 4Å: Chain A: N.218, Y.219, K.220, D.221 Chain B: R.87 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.220, A:D.221 Salt bridges: B:R.87 ACT.12: 7 residues within 4Å: Chain A: G.75, T.76, D.508, K.511, T.512 Chain B: N.80 Ligands: ACT.13 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:N.80, A:T.512 Hydrophobic interactions: A:D.508, A:K.511 Salt bridges: A:K.511 ACT.13: 4 residues within 4Å: Chain A: L.77, S.78, R.165 Ligands: ACT.12 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.165 ACT.24: 4 residues within 4Å: Chain B: I.211, N.212, L.256, N.257 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.212, B:N.212 ACT.25: 3 residues within 4Å: Chain B: K.150, Y.151, A.152 No protein-ligand interaction detected (PLIP) ACT.26: 4 residues within 4Å: Chain B: K.381, T.382, F.448, I.450 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.382

2 x CXS: 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID(Non-covalent)

CXS.14: 9 residues within 4Å: Chain A: E.206, D.209, K.213, Y.463, H.467, S.485, W.488, F.509, R.517 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.463, A:W.488, A:W.488, A:F.509 Salt bridges: A:K.213, A:H.467, A:R.517 CXS.27: 9 residues within 4Å: Chain B: E.206, D.209, K.213, Y.463, H.467, S.485, W.488, F.509, R.517 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:W.488, B:F.509 Salt bridges: B:K.213, B:H.467, B:R.517

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

2017-03-29

Peptides

Type II NADH:ubiquinone oxidoreductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
H

Type II NADH:ubiquinone oxidoreductase

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