SMTL ID : 3e39.1

Crystal structure of a putative nitroreductase in complex with fmn (dde_0787) from desulfovibrio desulfuricans subsp. at 1.70 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

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

ACT.1: 7 residues within 4Å: Chain A: L.45, Y.92, K.96 Chain B: G.123, E.124 Ligands: ACT.2, FMN.5 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.45 Hydrogen bonds: A:Y.92 Salt bridges: A:K.96 Water bridges: B:N.127 ACT.2: 5 residues within 4Å: Chain A: G.44, L.45 Chain B: Y.71 Ligands: ACT.1, FMN.5 1 PLIP interactions: 1 interactions with chain B Water bridges: B:Y.71 ACT.4: 7 residues within 4Å: Chain A: G.123, E.124 Chain B: G.44, L.45, Y.92, K.96 Ligands: FMN.3 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.45 Hydrogen bonds: B:Y.92 Water bridges: B:K.96 Salt bridges: B:K.96

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.3: 21 residues within 4Å: Chain A: R.15, R.16, S.17, R.19, Y.71, I.74, V.120, W.121, L.122, G.123, E.124, S.160, R.162 Chain B: P.42, S.43, G.44, N.46, Y.92, K.96, Q.99 Ligands: ACT.4 22 PLIP interactions: 20 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:W.121, A:W.121, A:W.121, B:K.96 Hydrogen bonds: A:S.17, A:S.17, A:S.17, A:S.17, A:R.19, A:R.19, A:Y.71, A:G.123, A:E.124, A:S.160, B:G.44 Water bridges: A:R.19, A:I.125 Salt bridges: A:R.15, A:R.16, A:R.162 pi-Stacking: A:Y.71, A:W.121 FMN.5: 21 residues within 4Å: Chain A: P.42, S.43, G.44, N.46, Y.92, K.96 Chain B: R.15, R.16, S.17, R.19, Y.71, I.74, V.120, W.121, L.122, G.123, E.124, S.160, R.162 Ligands: ACT.1, ACT.2 21 PLIP interactions: 19 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:W.121, B:W.121, A:K.96 Hydrogen bonds: B:S.17, B:S.17, B:S.17, B:S.17, B:R.19, B:R.19, B:G.123, B:E.124, B:S.160, B:S.160, A:S.43 Water bridges: B:R.19, B:I.125 Salt bridges: B:R.15, B:R.16, B:R.162 pi-Stacking: B:Y.71, B:W.121

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

PGE.6: 4 residues within 4Å: Chain A: N.46 Chain B: S.159, S.160, S.161 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.46, B:S.161

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of Putative Nitroreductase in Complex with FMN (YP_387283.1) from DESULFOVIBRIO DESULFURICANS G20 at 1.70 A resolution. To be published

Release Date

2008-08-19

Peptides

Putative Nitroreductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Putative Nitroreductase