SMTL ID : 4b2o.1

Crystal structure of Bacillus subtilis YmdB, a global regulator of late adaptive responses.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.64 Å

Oligo State

homo-tetramer

Ligands

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 8 residues within 4Å: Chain A: E.39, N.40, N.67, H.68, H.175, H.177 Ligands: FE2.2, FE2.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.67 Salt bridges: A:H.68, A:H.175, A:H.177 PO4.4: 8 residues within 4Å: Chain B: E.39, N.40, N.67, H.68, H.175, H.177 Ligands: FE2.5, FE2.6 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.40, B:N.40 Water bridges: B:H.68, B:H.175 Salt bridges: B:H.68, B:H.175, B:H.177 PO4.7: 8 residues within 4Å: Chain C: E.39, N.40, N.67, H.68, H.175, H.177 Ligands: FE2.8, FE2.9 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.67 Salt bridges: C:H.68, C:H.175, C:H.177 PO4.10: 8 residues within 4Å: Chain D: E.39, N.40, N.67, H.68, H.175, H.177 Ligands: FE2.11, FE2.12 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:N.40, D:N.40, D:N.67, D:H.175 Salt bridges: D:H.68, D:H.175, D:H.177

8 x FE2: FE (II) ION(Non-covalent)

FE2.2: 6 residues within 4Å: Chain A: D.8, E.39, N.40, H.177 Ligands: PO4.1, FE2.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.8, A:E.39, A:H.177, H2O.1 FE2.3: 6 residues within 4Å: Chain A: E.39, N.67, H.150, H.175 Ligands: PO4.1, FE2.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.39, A:H.150, A:H.175, H2O.1 FE2.5: 6 residues within 4Å: Chain B: D.8, E.39, N.40, H.177 Ligands: PO4.4, FE2.6 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.8, B:E.39, B:H.177, H2O.17 FE2.6: 6 residues within 4Å: Chain B: E.39, N.67, H.150, H.175 Ligands: PO4.4, FE2.5 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.39, B:H.150, B:H.175, H2O.17 FE2.8: 6 residues within 4Å: Chain C: E.39, N.67, H.150, H.175 Ligands: PO4.7, FE2.9 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.39, C:H.150, C:H.175, H2O.31 FE2.9: 7 residues within 4Å: Chain C: D.8, E.39, N.40, H.150, H.177 Ligands: PO4.7, FE2.8 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.8, C:E.39, C:H.177, H2O.31 FE2.11: 6 residues within 4Å: Chain D: E.39, N.67, H.150, H.175 Ligands: PO4.10, FE2.12 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.39, D:H.150, D:H.175, H2O.45 FE2.12: 6 residues within 4Å: Chain D: D.8, E.39, N.40, H.177 Ligands: PO4.10, FE2.11 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.8, D:E.39, D:H.177, H2O.45

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Diethmaier, C. et al., The Ymdb Phosphodiesterase is a Global Regulator of Late Adaptive Responses in Bacillus Subtilis. J.Bacteriol. (2014)

Release Date

2013-07-24

Peptides

YMDB PHOSPHODIESTERASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

YMDB PHOSPHODIESTERASE