SMTL ID : 3h4o.1

Crystal structure of a nitroreductase family protein (cd3355) from clostridium difficile 630 at 1.50 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 23 residues within 4Å: Chain A: R.29, Y.30, S.31, R.33, Y.85, V.134, W.135, V.136, C.137, Y.138, E.170, R.174, R.179 Chain B: P.56, T.57, G.58, G.59, N.60, L.110, I.113, D.114, I.117 Ligands: MPD.2 24 PLIP interactions: 5 interactions with chain B, 19 interactions with chain A Hydrophobic interactions: B:L.110, B:I.113, B:I.117, A:W.135, A:W.135 Hydrogen bonds: B:G.59, A:S.31, A:S.31, A:S.31, A:S.31, A:R.33, A:R.33, A:Y.85, A:C.137, A:Y.138 Water bridges: B:G.59, A:R.29, A:R.33, A:R.33, A:R.174, A:R.179 Salt bridges: A:R.29, A:R.174, A:R.179 FMN.4: 23 residues within 4Å: Chain A: P.56, T.57, G.58, G.59, N.60, L.110, I.113, D.114, I.117 Chain B: R.29, Y.30, S.31, R.33, Y.85, V.134, W.135, V.136, C.137, Y.138, E.170, R.174, R.179 Ligands: MPD.5 25 PLIP interactions: 5 interactions with chain A, 20 interactions with chain B Hydrophobic interactions: A:L.110, A:I.113, A:I.117, B:W.135, B:W.135 Hydrogen bonds: A:G.59, B:S.31, B:S.31, B:S.31, B:S.31, B:R.33, B:R.33, B:Y.85, B:Y.85, B:C.137, B:Y.138 Water bridges: A:G.59, B:R.29, B:R.33, B:R.33, B:R.174, B:R.179 Salt bridges: B:R.29, B:R.174, B:R.179

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

MPD.2: 5 residues within 4Å: Chain A: Y.138 Chain B: G.58, G.59, W.101 Ligands: FMN.1 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:W.101, A:Y.138 Hydrogen bonds: B:G.59 MPD.5: 5 residues within 4Å: Chain A: G.58, G.59, W.101 Chain B: Y.138 Ligands: FMN.4 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:W.101, B:Y.138 Hydrogen bonds: A:G.59

2 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.3: 5 residues within 4Å: Chain A: A.81, A.82, N.83, Y.138 Chain B: F.105 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:N.83, A:Y.138, B:F.105 Water bridges: A:A.81, A:N.83 MRD.6: 5 residues within 4Å: Chain A: F.105 Chain B: A.81, A.82, N.83, Y.138 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:N.83, B:Y.138, A:F.105 Water bridges: B:A.81, B:N.83

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of NITROREDUCTASE FAMILY PROTEIN (YP_001089872.1) from CLOSTRIDIUM DIFFICILE 630 at 1.50 A resolution. To be published

Release Date

2009-05-19

Peptides

NITROREDUCTASE FAMILY PROTEIN: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

NITROREDUCTASE FAMILY PROTEIN

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