SMTL ID : 3gr3.1

Crystal structure of a nitroreductase-like family protein (pnba, bh06130) from bartonella henselae str. houston-1 at 1.45 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-dimer

Ligands

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 25 residues within 4Å: Chain A: R.16, K.17, S.18, R.20, Y.85, V.100, N.125, Y.129, C.170, A.171, Q.172, A.173, A.174, T.214, R.216 Chain B: P.43, S.44, G.45, T.46, N.47, D.150, M.153 Ligands: UNL.2, EDO.4, EDO.11 21 PLIP interactions: 2 interactions with chain B, 19 interactions with chain A Hydrogen bonds: B:S.44, B:T.46, A:S.18, A:S.18, A:S.18, A:R.20, A:R.20, A:Y.85, A:N.125, A:A.173, A:A.174, A:T.214 Hydrophobic interactions: A:A.171, A:A.173 Water bridges: A:R.16, A:R.20, A:Y.129, A:T.214, A:R.216 Salt bridges: A:R.16, A:R.216 FMN.8: 25 residues within 4Å: Chain A: P.43, S.44, G.45, T.46, N.47, D.150, M.153 Chain B: R.16, K.17, S.18, R.20, Y.85, V.100, N.125, Y.129, C.170, A.171, Q.172, A.173, A.174, T.214, R.216 Ligands: EDO.6, UNL.9, EDO.12 19 PLIP interactions: 17 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:A.171, B:A.173 Hydrogen bonds: B:S.18, B:S.18, B:S.18, B:R.20, B:R.20, B:N.125, B:Y.129, B:A.173, B:A.174, A:S.44, A:T.46 Water bridges: B:N.125, B:N.125, B:T.214, B:R.216 Salt bridges: B:R.16, B:R.216

2 x UNL: UNKNOWN LIGAND

UNL.2: 10 residues within 4Å: Chain A: R.80, Y.85, K.122, F.126, A.174, D.177 Chain B: G.45, T.46 Ligands: FMN.1, EDO.4 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.80, A:R.80, A:Y.85, A:K.122, A:K.122, A:D.177, B:T.46 Water bridges: A:N.125 UNL.9: 10 residues within 4Å: Chain A: G.45, T.46 Chain B: R.80, Y.85, K.122, F.126, A.174, D.177 Ligands: FMN.8, EDO.12 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.80, B:R.80, B:Y.85, B:D.177, A:T.46 Water bridges: B:Y.129

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 3 residues within 4Å: Chain A: R.80, Y.84, Y.85 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain B: R.80, Y.84, Y.85 Ligand excluded by PLIP

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

EDO.4: 5 residues within 4Å: Chain A: R.20, V.100, G.101 Ligands: FMN.1, UNL.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.100 Water bridges: A:N.125 EDO.5: 5 residues within 4Å: Chain A: L.14, S.15, R.16, K.17 Chain B: R.41 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:R.41, A:T.214 Water bridges: A:S.15, A:T.214, A:T.214 EDO.6: 9 residues within 4Å: Chain A: G.45, L.48, P.50, G.146, S.147, D.150 Chain B: Y.84, Y.85 Ligands: FMN.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.45 Water bridges: A:S.147 EDO.11: 9 residues within 4Å: Chain A: Y.84, Y.85 Chain B: G.45, L.48, P.50, G.146, S.147, D.150 Ligands: FMN.1 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.45 Water bridges: B:S.147 EDO.12: 5 residues within 4Å: Chain B: R.20, V.100, G.101 Ligands: FMN.8, UNL.9 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.100 Water bridges: B:N.125 EDO.13: 5 residues within 4Å: Chain B: E.215, R.216, E.217, P.218, N.221 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.215, B:N.221 Water bridges: B:E.217 EDO.14: 4 residues within 4Å: Chain B: R.163, G.166, D.168, R.203 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.163, B:R.163, B:G.166 Water bridges: B:S.15, B:G.166, B:D.168, B:R.203

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

ACT.7: 2 residues within 4Å: Chain A: G.164, F.165 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.165 Hydrogen bonds: A:G.164 ACT.15: 4 residues within 4Å: Chain A: F.10 Chain B: E.34, L.38, F.165 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.10 Water bridges: B:E.34

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of nitroreductase-like family protein (YP_033442.1) from BARTONELLA HENSELAE HOUSTON-1 at 1.45 A resolution. To be published

Release Date

2009-04-07

Peptides

Nitroreductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Nitroreductase