SMTL ID : 3bem.1

Crystal structure of putative nitroreductase ydfN (2632848) from Bacillus subtilis at 1.65 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-dimer

Ligands

1 x NI: NICKEL (II) ION(Non-covalent)

NI.1: 3 residues within 4Å: Chain A: H.18, E.22 Chain B: H.12 5 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:H.18, A:E.22, A:E.22, B:H.12, H2O.13

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

ACT.2: 4 residues within 4Å: Chain A: F.54, Y.106, M.123 Ligands: FMN.5 No protein-ligand interaction detected (PLIP)

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.3: 19 residues within 4Å: Chain A: R.23, R.24, S.25, Q.80, K.82, C.166, P.167, M.168, I.169, G.170, R.205, R.208 Chain B: P.51, S.52, A.53, F.54, N.55, N.146, L.149 20 PLIP interactions: 16 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:I.169, B:A.53, B:L.149 Hydrogen bonds: A:S.25, A:S.25, A:S.25, A:S.25, A:Q.80, A:Q.80, A:K.82, A:I.169, A:G.170, B:S.52, B:F.54 Water bridges: A:R.24, A:R.24 Salt bridges: A:R.23, A:R.24, A:R.205, A:R.208 FMN.5: 20 residues within 4Å: Chain A: P.51, S.52, A.53, F.54, N.55, N.146, L.149 Chain B: R.23, R.24, S.25, Q.80, K.82, C.166, P.167, M.168, I.169, G.170, R.205, R.208 Ligands: ACT.2 20 PLIP interactions: 15 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:P.167, B:I.169, A:A.53, A:L.149 Hydrogen bonds: B:S.25, B:S.25, B:S.25, B:Q.80, B:Q.80, B:I.169, B:G.170, A:S.52, A:F.54, A:N.55 Water bridges: B:R.24, B:R.24 Salt bridges: B:R.23, B:R.24, B:R.205, B:R.208

2 x PGO: S-1,2-PROPANEDIOL(Non-covalent)

PGO.4: 8 residues within 4Å: Chain A: L.30, S.31, G.32, H.33, P.34, S.85, S.86, S.87 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.30, A:G.32, A:H.33 PGO.6: 4 residues within 4Å: Chain B: P.34, I.35, L.65, S.87 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.65 Hydrogen bonds: B:I.35, B:I.35

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of putative nitroreductase ydfN (2632848) from Bacillus subtilis at 1.65 A resolution. To be published

Release Date

2007-12-04

Peptides

Putative NAD(P)H nitroreductase ydfN: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Putative NAD(P)H nitroreductase ydfN