SMTL ID : 3ek3.1

Crystal structure of Nitroreductase with Bound FMN (YP_211706.1) from Bacteroides fragilis NCTC 9343 at 1.70 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 20 residues within 4Å: Chain A: R.14, R.15, S.16, R.18, Y.92, C.132, W.133, I.134, N.135, Q.136, K.179 Chain B: P.41, S.42, G.43, H.45, W.108, D.112 Ligands: UNL.2, MPD.3, MPD.5 19 PLIP interactions: 16 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:W.133, A:W.133, B:P.41, B:W.108 Hydrogen bonds: A:S.16, A:S.16, A:S.16, A:R.18, A:R.18, A:Y.92, A:N.135, A:Q.136, B:S.42 Water bridges: A:R.15, A:R.18 Salt bridges: A:R.14, A:R.15, A:K.179 pi-Stacking: A:W.133 FMN.6: 20 residues within 4Å: Chain A: P.41, S.42, G.43, H.45, W.108, D.112 Chain B: R.14, R.15, S.16, R.18, Y.92, C.132, W.133, I.134, N.135, Q.136, K.179 Ligands: UNL.7, MPD.8, MPD.10 20 PLIP interactions: 17 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:W.133, B:W.133, A:P.41, A:W.108 Hydrogen bonds: B:S.16, B:S.16, B:S.16, B:R.18, B:R.18, B:Y.92, B:Y.92, B:N.135, B:Q.136, A:S.42 Water bridges: B:R.15, B:R.18 Salt bridges: B:R.14, B:R.15, B:K.179 pi-Stacking: B:W.133

2 x UNL: UNKNOWN LIGAND

UNL.2: 9 residues within 4Å: Chain A: R.82, Y.92, N.135, Q.136 Chain B: G.43, M.44, W.108 Ligands: FMN.1, MPD.5 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.82, A:Y.92, A:Y.92, A:N.135, A:Q.136 UNL.7: 9 residues within 4Å: Chain A: G.43, M.44, W.108 Chain B: R.82, Y.92, N.135, Q.136 Ligands: FMN.6, MPD.10 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.82, B:Y.92, B:N.135, B:Q.136 Water bridges: B:Y.92

6 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.3: 4 residues within 4Å: Chain A: R.15, K.179 Chain B: H.45 Ligands: FMN.1 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:K.179, B:H.45 Hydrogen bonds: A:R.15 Water bridges: A:S.16, A:R.18 MPD.4: 4 residues within 4Å: Chain A: G.138, V.161, Y.162 Chain B: W.107 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Y.162, B:W.107, B:W.107 Hydrogen bonds: A:G.138 MPD.5: 4 residues within 4Å: Chain A: R.18 Chain B: M.44 Ligands: FMN.1, UNL.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.18 Water bridges: A:R.18 MPD.8: 4 residues within 4Å: Chain A: H.45 Chain B: R.15, K.179 Ligands: FMN.6 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:K.179, A:H.45 Hydrogen bonds: B:R.15 Water bridges: B:S.16, B:R.18 MPD.9: 4 residues within 4Å: Chain A: W.107 Chain B: G.138, V.161, Y.162 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Y.162, A:W.107, A:W.107 Hydrogen bonds: B:G.138 MPD.10: 4 residues within 4Å: Chain A: M.44 Chain B: R.18 Ligands: FMN.6, UNL.7 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.18 Water bridges: B:R.18

Links

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Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of Nitroreductase with Bound FMN (YP_211706.1) from Bacteroides fragilis NCTC 9343 at 1.70 A resolution. To be published

Release Date

2008-10-14

Peptides

Nitroreductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Nitroreductase