SMTL ID : 5yjw.1

Structure of the Ndi1 protein from Saccharomyces cerevisiae in complex with the competitive inhibitor, stigmatellin.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

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

FAD.1: 39 residues within 4Å: Chain A: G.31, S.32, G.33, W.34, G.35, I.53, S.54, P.55, R.56, T.62, P.63, L.65, P.66, E.99, A.100, A.146, V.147, G.148, L.166, K.167, T.210, R.315, V.317, G.353, D.354, P.362, T.363, A.364, Q.365, A.367, Y.453 Ligands: MG.2, MG.3, MG.4, MG.5, GOL.8, PEG.15, MES.23, SMA.26 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:L.65, A:P.66, A:K.167, A:T.210 Hydrogen bonds: A:S.32, A:S.32, A:W.34, A:G.35, A:S.54, A:T.62, A:T.62, A:A.100, A:A.100, A:D.354, A:P.362, A:A.364, A:Q.365 Water bridges: A:R.56, A:A.149, A:E.168, A:E.168, A:E.168, A:R.315, A:R.315, A:A.367 FAD.27: 39 residues within 4Å: Chain B: G.31, S.32, G.33, W.34, G.35, I.53, S.54, P.55, R.56, T.62, P.63, L.65, P.66, E.99, A.100, A.146, V.147, G.148, L.166, K.167, T.210, R.315, V.317, G.353, D.354, P.362, T.363, A.364, Q.365, A.367, Y.453 Ligands: MG.28, MG.29, MG.30, MG.31, GOL.34, PEG.41, MES.49, SMA.52 26 PLIP interactions: 26 interactions with chain B Hydrophobic interactions: B:L.65, B:P.66, B:K.167, B:T.210 Hydrogen bonds: B:S.32, B:S.32, B:W.34, B:G.35, B:S.54, B:T.62, B:A.100, B:A.100, B:D.354, B:P.362, B:A.364, B:Q.365 Water bridges: B:R.56, B:E.99, B:A.149, B:E.168, B:E.168, B:E.168, B:R.315, B:R.315, B:A.367, B:Y.453

8 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 8 residues within 4Å: Chain A: A.146, V.147, G.148, I.352, G.353, D.354, N.355 Ligands: FAD.1 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:I.352, FAD.1 MG.3: 7 residues within 4Å: Chain A: S.32, G.33, W.34, G.35, A.36, A.146 Ligands: FAD.1 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:A.146, FAD.1 MG.4: 3 residues within 4Å: Chain A: R.56, T.62 Ligands: FAD.1 No protein-ligand interaction detected (PLIP) MG.5: 5 residues within 4Å: Chain A: G.148, A.149, K.167, D.354 Ligands: FAD.1 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.354, H2O.1 MG.28: 8 residues within 4Å: Chain B: A.146, V.147, G.148, I.352, G.353, D.354, N.355 Ligands: FAD.27 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:I.352, FAD.27 MG.29: 7 residues within 4Å: Chain B: S.32, G.33, W.34, G.35, A.36, A.146 Ligands: FAD.27 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:A.146, FAD.27 MG.30: 3 residues within 4Å: Chain B: R.56, T.62 Ligands: FAD.27 No protein-ligand interaction detected (PLIP) MG.31: 5 residues within 4Å: Chain B: G.148, A.149, K.167, D.354 Ligands: FAD.27 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.354, H2O.14

2 x PE4: 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL(Non-functional Binders)

PE4.6: 20 residues within 4Å: Chain A: L.183, E.184, N.187, Y.221, F.229, L.230, K.477, R.478, D.479, F.480, F.481 Chain B: P.8, T.9, S.10, F.11, P.81, V.83, N.84, R.461 Ligands: MES.24 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:P.81, A:F.481 Hydrogen bonds: B:N.84 Water bridges: A:K.477 PE4.32: 20 residues within 4Å: Chain A: P.8, T.9, S.10, F.11, P.81, V.83, N.84, R.461 Chain B: L.183, E.184, N.187, Y.221, F.229, L.230, K.477, R.478, D.479, F.480, F.481 Ligands: MES.50 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.481, A:P.81 Water bridges: B:K.477 Hydrogen bonds: A:N.84

2 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)

P6G.7: 5 residues within 4Å: Chain A: R.450, F.467, A.474, F.475 Ligands: SMA.25 No protein-ligand interaction detected (PLIP) P6G.33: 5 residues within 4Å: Chain B: R.450, F.467, A.474, F.475 Ligands: SMA.51 No protein-ligand interaction detected (PLIP)

14 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 8 residues within 4Å: Chain A: P.209, M.251, T.363, A.417, L.418 Ligands: FAD.1, MES.23, SMA.26 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.418 GOL.9: 6 residues within 4Å: Chain A: S.331, K.332, R.333, G.334, A.336, F.357 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.332, A:R.333, A:G.334, A:G.334 GOL.10: 8 residues within 4Å: Chain A: L.173, R.177, K.482, G.483, L.484 Chain B: G.483, L.484 Ligands: GOL.36 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.177, A:K.482, B:G.483 Water bridges: A:L.484, A:L.484, A:L.484, B:K.76 GOL.11: 7 residues within 4Å: Chain A: A.244, R.274, T.275, A.276, K.288, T.289, K.290 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.274, A:A.276, A:K.290 GOL.20: 9 residues within 4Å: Chain A: D.220, Q.224, Y.420, E.424, F.446, R.450, L.473, R.478 Ligands: SMA.25 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Q.224, A:Y.420, A:E.424, A:R.450, A:R.478 Water bridges: A:E.217, A:D.220, A:D.220, A:L.473 GOL.21: 9 residues within 4Å: Chain A: G.207, G.208, E.243, L.245, I.247, V.248, L.249, N.250, M.251 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:I.247, A:L.249, A:N.250 Water bridges: A:G.207, A:E.243 GOL.22: 4 residues within 4Å: Chain A: P.55, R.56, E.168 Ligands: PG4.38 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.55, A:E.168 Water bridges: A:I.169 GOL.34: 8 residues within 4Å: Chain B: P.209, M.251, T.363, A.417, L.418 Ligands: FAD.27, MES.49, SMA.52 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.418 GOL.35: 6 residues within 4Å: Chain B: S.331, K.332, R.333, G.334, A.336, F.357 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.332, B:R.333, B:G.334, B:G.334 GOL.36: 8 residues within 4Å: Chain A: G.483, L.484 Chain B: L.173, R.177, K.482, G.483, L.484 Ligands: GOL.10 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.177, B:K.482, A:G.483 Water bridges: B:L.484, A:K.76 GOL.37: 7 residues within 4Å: Chain B: A.244, R.274, T.275, A.276, K.288, T.289, K.290 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.274, B:A.276, B:K.290 GOL.46: 9 residues within 4Å: Chain B: D.220, Q.224, Y.420, E.424, F.446, R.450, L.473, R.478 Ligands: SMA.51 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Q.224, B:Y.420, B:Y.420, B:R.450, B:R.478 Water bridges: B:E.217, B:L.473 GOL.47: 9 residues within 4Å: Chain B: G.207, G.208, E.243, L.245, I.247, V.248, L.249, N.250, M.251 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:I.247, B:L.249, B:N.250 Water bridges: B:G.207, B:E.243 GOL.48: 4 residues within 4Å: Chain B: P.55, R.56, E.168 Ligands: PG4.12 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:P.55, B:Y.58 Water bridges: B:I.169

4 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.12: 10 residues within 4Å: Chain A: F.481, L.484 Chain B: T.9, P.55, R.56, S.57, Y.58, I.79, E.97 Ligands: GOL.48 6 PLIP interactions: 1 interactions with chain A, 5 interactions with chain B Water bridges: A:K.482, B:Y.58, B:Y.58 Hydrogen bonds: B:P.55, B:S.57, B:S.57 PG4.13: 9 residues within 4Å: Chain A: D.23, P.25, D.141, Y.142, N.347, N.348, F.387, Q.388, K.389 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.348 PG4.38: 10 residues within 4Å: Chain A: T.9, P.55, R.56, S.57, Y.58, I.79, E.97 Chain B: F.481, L.484 Ligands: GOL.22 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:P.55, A:S.57, A:S.57 Water bridges: A:Y.58, B:K.482 PG4.39: 9 residues within 4Å: Chain B: D.23, P.25, D.141, Y.142, N.347, N.348, F.387, Q.388, K.389 1 PLIP interactions: 1 interactions with chain B Water bridges: B:N.348

6 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.14: 3 residues within 4Å: Chain A: Y.259, G.440, G.441 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.441 PEG.15: 6 residues within 4Å: Chain A: P.55, E.99, R.315, P.316, V.317 Ligands: FAD.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.317 Water bridges: A:R.315 PEG.18: 10 residues within 4Å: Chain A: F.154, I.156, V.205, V.242, E.243, A.244, T.275, A.276, V.277, W.308 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.242 Water bridges: A:A.244 PEG.40: 3 residues within 4Å: Chain B: Y.259, G.440, G.441 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.441 PEG.41: 6 residues within 4Å: Chain B: P.55, E.99, R.315, P.316, V.317 Ligands: FAD.27 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.317 Water bridges: B:R.315 PEG.44: 10 residues within 4Å: Chain B: F.154, I.156, V.205, V.242, E.243, A.244, T.275, A.276, V.277, W.308 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.242 Water bridges: B:A.244

6 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.16: 3 residues within 4Å: Chain A: S.455, R.463 Ligands: PGE.17 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.455 PGE.17: 5 residues within 4Å: Chain A: A.460, R.463, F.467 Ligands: PGE.16, PGE.45 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.463 PGE.19: 3 residues within 4Å: Chain A: F.475 Ligands: PGE.43, PGE.45 No protein-ligand interaction detected (PLIP) PGE.42: 3 residues within 4Å: Chain B: S.455, R.463 Ligands: PGE.43 1 PLIP interactions: 1 interactions with chain B Water bridges: B:S.455 PGE.43: 5 residues within 4Å: Chain B: A.460, R.463, F.467 Ligands: PGE.19, PGE.42 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.463 PGE.45: 3 residues within 4Å: Chain B: F.475 Ligands: PGE.17, PGE.19 No protein-ligand interaction detected (PLIP)

4 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.23: 10 residues within 4Å: Chain A: L.166, G.208, P.209, T.210, A.309, T.310, G.311, N.312 Ligands: FAD.1, GOL.8 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.210, A:T.210, A:T.210 Water bridges: A:G.211 MES.24: 9 residues within 4Å: Chain A: K.228, F.229, L.230, P.231 Chain B: K.12, T.13, M.14, V.83 Ligands: PE4.6 No protein-ligand interaction detected (PLIP) MES.49: 10 residues within 4Å: Chain B: L.166, G.208, P.209, T.210, A.309, T.310, G.311, N.312 Ligands: FAD.27, GOL.34 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.210, B:T.210, B:T.210 Water bridges: B:G.211 MES.50: 9 residues within 4Å: Chain A: K.12, T.13, M.14, V.83 Chain B: K.228, F.229, L.230, P.231 Ligands: PE4.32 No protein-ligand interaction detected (PLIP)

4 x SMA: STIGMATELLIN A(Non-covalent)

SMA.25: 5 residues within 4Å: Chain A: F.446, Y.447, R.450 Ligands: P6G.7, GOL.20 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.450 Water bridges: A:R.450 pi-Stacking: A:Y.447 SMA.26: 15 residues within 4Å: Chain A: W.34, P.63, A.364, Q.365, H.368, L.415, G.416, A.417, L.418, I.430, S.432, L.452, M.456 Ligands: FAD.1, GOL.8 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Q.365, A:L.415, A:L.415, A:L.418, A:I.430, A:I.430, A:L.452 SMA.51: 5 residues within 4Å: Chain B: F.446, Y.447, R.450 Ligands: P6G.33, GOL.46 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.450 Water bridges: B:R.450 pi-Stacking: B:Y.447 SMA.52: 15 residues within 4Å: Chain B: W.34, P.63, A.364, Q.365, H.368, L.415, G.416, A.417, L.418, I.430, S.432, L.452, M.456 Ligands: FAD.27, GOL.34 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:Q.365, B:L.415, B:L.415, B:L.418, B:I.430, B:I.430, B:L.452

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yamashita, T. et al., Ubiquinone binding site of yeast NADH dehydrogenase revealed by structures binding novel competitive- and mixed-type inhibitors. Sci Rep (2018)

Release Date

2018-02-14

Peptides

Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial