SMTL ID : 1y7m.1

Crystal Structure of the B. subtilis YkuD protein at 2 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-dimer

Ligands

2 x CD: CADMIUM ION(Non-covalent)

CD.1: 3 residues within 4Å: Chain A: H.119, C.139 Ligands: SO4.2 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.139, H2O.1 CD.3: 3 residues within 4Å: Chain B: H.119, C.139 Ligands: SO4.4 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.139, H2O.3

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 7 residues within 4Å: Chain A: H.123, S.136, K.137, G.138, C.139, R.141 Ligands: CD.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.137, A:G.138, A:C.139 Salt bridges: A:H.123, A:R.141 SO4.4: 7 residues within 4Å: Chain B: H.123, S.136, K.137, G.138, C.139, R.141 Ligands: CD.3 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.137, B:G.138, B:C.139 Salt bridges: B:H.123, B:R.141 SO4.5: 4 residues within 4Å: Chain A: R.159 Chain B: E.94, Y.96, R.159 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:Y.96, A:N.73 Salt bridges: B:R.159, A:R.159 Water bridges: A:H.57, A:R.159 SO4.6: 2 residues within 4Å: Chain B: H.143, K.145 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.145

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bielnicki, J. et al., B. subtilis ykuD protein at 2.0 A resolution: insights into the structure and function of a novel, ubiquitous family of bacterial enzymes. Proteins (2006)

Release Date

2005-03-01

Peptides

hypothetical protein BSU14040: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

hypothetical protein BSU14040