SMTL ID : 3lzw.1

Crystal structure of ferredoxin-NADP+ oxidoreductase from bacillus subtilis (form I)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

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

FAD.1: 33 residues within 4Å: Chain A: I.13, G.14, G.15, G.16, P.17, V.18, I.36, E.37, S.38, G.44, Q.45, L.46, Y.50, I.55, D.57, Q.88, A.89, V.90, T.118, A.119, G.120, G.122, A.123, F.124, I.255, G.284, D.285, N.294, L.295, I.296 Chain B: H.324, S.325, T.326 30 PLIP interactions: 27 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:Y.50 Hydrogen bonds: A:G.15, A:G.16, A:V.18, A:G.19, A:S.38, A:G.44, A:Q.45, A:Q.45, A:Y.50, A:Y.50, A:D.57, A:V.90, A:V.90, A:N.121, A:F.124, A:D.285, A:N.294, A:I.296, B:S.325, B:T.326 Water bridges: A:G.120, A:N.121, A:A.123, A:A.123, A:I.286, A:A.297, A:G.299 pi-Stacking: A:Y.50, B:H.324 FAD.5: 33 residues within 4Å: Chain A: H.324, S.325, T.326 Chain B: I.13, G.14, G.15, G.16, P.17, V.18, I.36, E.37, S.38, G.44, Q.45, L.46, Y.50, I.55, D.57, Q.88, A.89, V.90, T.118, A.119, G.120, G.122, A.123, F.124, I.255, G.284, D.285, N.294, L.295, I.296 30 PLIP interactions: 27 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:Y.50 Hydrogen bonds: B:G.15, B:G.16, B:V.18, B:G.19, B:S.38, B:G.44, B:Q.45, B:Q.45, B:Y.50, B:Y.50, B:D.57, B:V.90, B:V.90, B:N.121, B:F.124, B:D.285, B:N.294, B:I.296, A:S.325, A:T.326 Water bridges: B:G.120, B:N.121, B:A.123, B:A.123, B:I.286, B:A.297, B:G.299 pi-Stacking: B:Y.50, A:H.324

2 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.2: 18 residues within 4Å: Chain A: A.48, L.49, E.52, G.162, G.163, D.164, S.165, D.168, H.184, R.185, R.186, R.190, H.192, N.245, Y.246, G.247, F.248 Ligands: NA.4 34 PLIP interactions: 34 interactions with chain A Hydrophobic interactions: A:D.164 Hydrogen bonds: A:G.162, A:G.162, A:S.165, A:S.165, A:D.168 Water bridges: A:E.52, A:K.53, A:G.161, A:G.163, A:G.163, A:D.164, A:D.164, A:D.164, A:D.164, A:R.185, A:R.190, A:R.190, A:R.190, A:R.190, A:R.190, A:G.247, A:G.247, A:F.248, A:F.248 Salt bridges: A:H.184, A:R.185, A:R.186, A:R.190, A:R.190 pi-Stacking: A:Y.246, A:Y.246 pi-Cation interactions: A:R.185, A:R.185 NAP.6: 18 residues within 4Å: Chain B: A.48, L.49, E.52, G.162, G.163, D.164, S.165, D.168, H.184, R.185, R.186, R.190, H.192, N.245, Y.246, G.247, F.248 Ligands: NA.8 34 PLIP interactions: 34 interactions with chain B Hydrophobic interactions: B:D.164 Hydrogen bonds: B:G.162, B:G.162, B:S.165, B:S.165, B:D.168 Water bridges: B:E.52, B:K.53, B:G.161, B:G.163, B:G.163, B:D.164, B:D.164, B:D.164, B:D.164, B:R.185, B:R.190, B:R.190, B:R.190, B:R.190, B:R.190, B:G.247, B:G.247, B:F.248, B:F.248 Salt bridges: B:H.184, B:R.185, B:R.186, B:R.190, B:R.190 pi-Stacking: B:Y.246, B:Y.246 pi-Cation interactions: B:R.185, B:R.185

4 x NA: SODIUM ION(Non-functional Binders)

NA.3: 2 residues within 4Å: Chain A: S.266, D.285 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.286 NA.4: 1 residues within 4Å: Ligands: NAP.2 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.164, A:D.164 NA.7: 2 residues within 4Å: Chain B: S.266, D.285 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:I.286 NA.8: 1 residues within 4Å: Ligands: NAP.6 3 PLIP interactions: 3 interactions with chain B Water bridges: B:D.164, B:R.190, B:R.190

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Komori, H. et al., Crystal structure analysis of Bacillus subtilis ferredoxin-NADP(+) oxidoreductase and the structural basis for its substrate selectivity. Protein Sci. (2010)

Release Date

2010-12-08

Peptides

Ferredoxin--NADP reductase 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Ferredoxin--NADP reductase 2

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