SMTL ID : 3gfa.1

Crystal structure of a putative nitroreductase in complex with fmn (cd3205) from clostridium difficile 630 at 1.35 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

homo-dimer

Ligands

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 19 residues within 4Å: Chain A: R.10, R.11, S.12, R.14, T.89, L.148, W.149, I.150, C.151, D.152, R.186, R.188 Chain B: P.37, S.38, S.39, N.41, A.124, S.128 Ligands: CL.7 25 PLIP interactions: 21 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:W.149, A:W.149, A:W.149, B:P.37 Hydrogen bonds: A:S.12, A:S.12, A:S.12, A:S.12, A:R.14, A:R.14, A:T.89, A:C.151, A:D.152, B:S.38 Water bridges: A:R.11, A:R.14, A:R.14, A:T.89, A:T.89, A:R.188, B:K.40, B:K.40 Salt bridges: A:R.10, A:R.186, A:R.188 FMN.6: 19 residues within 4Å: Chain A: P.37, S.38, S.39, N.41, A.124, S.128 Chain B: R.10, R.11, S.12, R.14, T.89, L.148, W.149, I.150, C.151, D.152, R.186, R.188 Ligands: CL.2 28 PLIP interactions: 21 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:W.149, B:W.149, B:W.149, A:P.37 Hydrogen bonds: B:S.12, B:S.12, B:S.12, B:S.12, B:R.14, B:R.14, B:T.89, B:C.151, B:D.152, A:S.38 Water bridges: B:R.14, B:R.14, B:T.89, B:T.89, B:R.186, B:R.188, A:K.40, A:K.40, A:K.40, A:K.40, A:N.41 Salt bridges: B:R.10, B:R.186, B:R.188

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

CL.2: 2 residues within 4Å: Chain A: K.40 Ligands: FMN.6 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain B: K.40 Ligands: FMN.1 Ligand excluded by PLIP

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: I.105, L.106, G.107, K.108 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.105, A:K.108, A:K.108 Water bridges: A:G.107 GOL.4: 6 residues within 4Å: Chain A: L.59, K.60, S.63, V.90, E.91, K.94 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.63, A:S.63, A:E.91 Water bridges: A:K.94 GOL.5: 6 residues within 4Å: Chain A: R.46, L.103, I.105, T.166, D.167, S.168 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.168, A:S.168 Water bridges: A:R.46, A:D.167, A:D.167, B:E.196

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

MPD.8: 10 residues within 4Å: Chain A: L.76, S.79, H.82, C.151, D.152, F.155 Chain B: K.40, F.120, Y.121, A.124 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.76, A:H.82, B:Y.121 Hydrogen bonds: A:D.152, A:D.152, B:F.120

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

MRD.9: 8 residues within 4Å: Chain A: S.39, K.40, R.42, F.120, Y.121 Chain B: C.151, D.152, F.155 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:Y.121, B:F.155 Hydrogen bonds: A:R.42, B:D.152, B:D.152

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_001089721.1) from CLOSTRIDIUM DIFFICILE 630 at 1.35 A resolution. To be published

Release Date

2009-03-17

Peptides

Putative nitroreductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Putative nitroreductase