SMTL ID : 1zch.1

Structure of the hypothetical oxidoreductase YcnD from Bacillus subtilis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

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

CL.1: 2 residues within 4Å: Chain B: I.41 Ligands: FMN.3 Ligand excluded by PLIP CL.4: 2 residues within 4Å: Chain A: I.41 Ligands: FMN.6 Ligand excluded by PLIP

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 2 residues within 4Å: Chain A: E.150 Chain B: N.189 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.150, H2O.12, H2O.13 CA.5: 2 residues within 4Å: Chain A: N.189 Chain B: E.150 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.150, H2O.2, H2O.3

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.3: 21 residues within 4Å: Chain A: H.11, R.12, S.13, R.15, Q.67, W.69, V.133, P.134, I.135, G.136, A.137, S.159, K.173, R.175 Chain B: P.38, S.39, S.40, N.42, V.112, I.116 Ligands: CL.1 22 PLIP interactions: 19 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:P.134, B:V.112, B:I.116 Hydrogen bonds: A:S.13, A:S.13, A:S.13, A:R.15, A:R.15, A:Q.67, A:Q.67, A:G.136, A:A.137, B:S.39 Water bridges: A:S.13, A:A.171, A:K.173, A:K.173, A:K.173, A:R.175 Salt bridges: A:H.11, A:K.173, A:R.175 FMN.6: 21 residues within 4Å: Chain A: P.38, S.39, S.40, N.42, V.112, I.116 Chain B: H.11, R.12, S.13, R.15, Q.67, W.69, V.133, P.134, I.135, G.136, A.137, S.159, K.173, R.175 Ligands: CL.4 22 PLIP interactions: 19 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:P.134, A:V.112, A:I.116 Hydrogen bonds: B:S.13, B:S.13, B:S.13, B:R.15, B:R.15, B:Q.67, B:Q.67, B:G.136, B:A.137, A:S.39 Water bridges: B:S.13, B:A.171, B:K.173, B:K.173, B:K.173, B:R.175 Salt bridges: B:H.11, B:K.173, B:R.175

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Morokutti, A. et al., Structure and Function of YcnD from Bacillus subtilis, a Flavin-Containing Oxidoreductase(,). Biochemistry (2005)

Release Date

2005-11-01

Peptides

Hypothetical oxidoreductase ycnD: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Hypothetical oxidoreductase ycnD