SMTL ID : 3iup.1

Crystal structure of Putative NADPH:quinone oxidoreductase (YP_296108.1) from RALSTONIA EUTROPHA JMP134 at 1.70 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.1: 26 residues within 4Å: Chain A: P.46, V.155, N.156, T.159, A.179, A.181, S.182, N.183, L.184, R.204, K.205, Q.208, A.247, T.248, Y.286, G.287, L.289, D.290, W.309, L.310, L.311, R.363, A.364, T.365, K.368 Ligands: ACT.5 38 PLIP interactions: 38 interactions with chain A Hydrophobic interactions: A:V.155, A:T.159, A:L.184, A:Y.286 Hydrogen bonds: A:N.156, A:A.181, A:N.183, A:L.184, A:R.204, A:Q.208, A:A.247, A:Y.286, A:Y.286, A:L.289, A:L.311, A:R.363, A:T.365 Water bridges: A:P.46, A:S.47, A:A.181, A:S.182, A:R.204, A:R.204, A:G.288, A:T.291, A:A.364, A:A.364, A:T.365, A:G.366, A:G.366, A:K.368, A:K.368 Salt bridges: A:R.204, A:K.205, A:K.368, A:K.368 pi-Cation interactions: A:R.204, A:R.204 NDP.8: 27 residues within 4Å: Chain B: N.45, P.46, V.155, N.156, T.159, A.179, A.181, S.182, N.183, L.184, R.204, K.205, Q.208, A.247, T.248, Y.286, G.287, L.289, D.290, W.309, L.310, L.311, R.363, A.364, T.365, K.368 Ligands: EDO.9 34 PLIP interactions: 34 interactions with chain B Hydrophobic interactions: B:V.155, B:T.159, B:L.184, B:Y.286 Hydrogen bonds: B:N.156, B:A.181, B:N.183, B:L.184, B:R.204, B:Q.208, B:A.247, B:Y.286, B:Y.286, B:L.289, B:L.311, B:R.363, B:T.365 Water bridges: B:S.47, B:A.179, B:S.182, B:Q.186, B:G.288, B:D.290, B:A.364, B:A.364, B:T.365, B:K.368, B:K.368 Salt bridges: B:R.204, B:K.205, B:K.368, B:K.368 pi-Cation interactions: B:R.204, B:R.204

9 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 4 residues within 4Å: Chain A: Q.186, Q.190, Q.215, A.339 1 PLIP interactions: 1 interactions with chain A Water bridges: A:A.339 EDO.3: 5 residues within 4Å: Chain A: W.309, L.310, P.313, F.314, K.317 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.310, A:K.317 Water bridges: A:K.317 EDO.4: 3 residues within 4Å: Chain A: S.4, S.24, D.26 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.4, A:S.24 EDO.9: 7 residues within 4Å: Chain A: Y.275 Chain B: S.47, N.96, V.155, L.310, L.311 Ligands: NDP.8 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.47, B:S.47, B:L.311, A:Y.275 EDO.10: 3 residues within 4Å: Chain B: Q.190, Q.215, A.339 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.339 Water bridges: B:Q.190 EDO.11: 6 residues within 4Å: Chain A: P.293 Chain B: K.252, E.295, F.296, N.297 Ligands: EDO.12 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.295 Water bridges: B:N.297 EDO.12: 6 residues within 4Å: Chain B: G.255, T.259, F.296, N.297, N.299 Ligands: EDO.11 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.259, B:N.299 EDO.13: 3 residues within 4Å: Chain B: G.319, R.320, E.321 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.320, B:R.320, B:R.320, B:E.321 Water bridges: B:G.319 EDO.14: 4 residues within 4Å: Chain B: D.136, C.138, F.154, K.327 2 PLIP interactions: 2 interactions with chain B Water bridges: B:Q.137, B:K.327

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

ACT.5: 7 residues within 4Å: Chain A: S.47, V.155, L.310, L.311, F.312 Chain B: Y.275 Ligands: NDP.1 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.312 Hydrogen bonds: A:S.47, A:L.311, B:Y.275 Water bridges: A:N.96 ACT.6: 7 residues within 4Å: Chain A: L.161, V.164, E.165, R.168, R.322, L.326 Ligands: ACT.7 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.161, A:E.165, A:L.326 Hydrogen bonds: A:E.165 Water bridges: A:R.322, A:R.322, A:R.329 Salt bridges: A:R.168, A:R.322 ACT.7: 4 residues within 4Å: Chain A: R.168, D.195, R.329 Ligands: ACT.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.195 Salt bridges: A:R.168

Links

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Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of Putative NADPH:quinone oxidoreductase (YP_296108.1) from RALSTONIA EUTROPHA JMP134 at 1.70 A resolution. To be published

Release Date

2009-09-15

Peptides

Putative NADPH:quinone oxidoreductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Putative NADPH:quinone oxidoreductase