SMTL ID : 3boy.1

Crystal structure of the HutP antitermination complex bound to the HUT mRNA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-hexamer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain B: H.72, H.76 Chain C: H.137 Ligands: HIS.3 5 PLIP interactions: 2 interactions with chain B, 1 Ligand-Ligand interactions, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: B:H.72, B:H.76, HIS.3, C:H.137, H2O.12 MG.5: 4 residues within 4Å: Chain C: H.72, H.76 Chain D: H.137 Ligands: HIS.4 5 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: C:H.72, C:H.76, D:H.137, HIS.4, H2O.11 MG.6: 4 residues within 4Å: Chain B: H.137 Chain D: H.72, H.76 Ligands: HIS.2 5 PLIP interactions: 1 Ligand-Ligand interactions, 1 interactions with chain B, 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: HIS.2, B:H.137, D:H.72, D:H.76, H2O.14 MG.7: 4 residues within 4Å: Chain F: H.72, H.76 Chain G: H.137 Ligands: HIS.9 5 PLIP interactions: 2 interactions with chain F, 1 interactions with chain G, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: F:H.72, F:H.76, G:H.137, HIS.9, H2O.27 MG.11: 4 residues within 4Å: Chain G: H.72, H.76 Chain H: H.137 Ligands: HIS.10 5 PLIP interactions: 2 interactions with chain G, 1 Ligand-Ligand interactions, 1 interactions with chain H, 1 Ligand-Water interactions Metal complexes: G:H.72, G:H.76, HIS.10, H:H.137, H2O.27 MG.12: 4 residues within 4Å: Chain F: H.137 Chain H: H.72, H.76 Ligands: HIS.8 5 PLIP interactions: 2 interactions with chain H, 1 Ligand-Ligand interactions, 1 interactions with chain F, 1 Ligand-Water interactions Metal complexes: H:H.72, H:H.76, HIS.8, F:H.137, H2O.30

6 x HIS: HISTIDINE(Non-covalent)

HIS.2: 12 residues within 4Å: Chain B: R.87, L.96, R.97, I.128, G.129, A.130, H.137 Chain D: Y.68, H.72, Y.75, H.76 Ligands: MG.6 10 PLIP interactions: 4 interactions with chain D, 5 interactions with chain B, 1 Ligand-Ligand interactions Hydrogen bonds: D:Y.68, D:H.76, B:L.96, B:A.130, H.2 Salt bridges: D:H.76, B:R.87, B:R.97, B:H.137 pi-Stacking: D:Y.75 HIS.3: 11 residues within 4Å: Chain B: Y.68, H.72, Y.75, H.76 Chain C: R.87, R.97, I.128, G.129, A.130, H.137 Ligands: MG.1 10 PLIP interactions: 4 interactions with chain B, 5 interactions with chain C, 1 Ligand-Ligand interactions Hydrogen bonds: B:Y.68, B:H.76, C:L.96, C:A.130, H.3 Salt bridges: B:H.76, C:R.87, C:R.97, C:H.137 pi-Stacking: B:Y.75 HIS.4: 11 residues within 4Å: Chain C: Y.68, H.72, Y.75, H.76 Chain D: R.87, R.97, I.128, G.129, A.130, H.137 Ligands: MG.5 8 PLIP interactions: 1 Ligand-Ligand interactions, 5 interactions with chain D, 2 interactions with chain C Hydrogen bonds: H.4, D:L.96, D:A.130, C:H.76 Salt bridges: D:R.87, D:R.97, D:H.137, C:H.76 HIS.8: 12 residues within 4Å: Chain F: R.87, L.96, R.97, I.128, G.129, A.130, H.137 Chain H: Y.68, H.72, Y.75, H.76 Ligands: MG.12 9 PLIP interactions: 3 interactions with chain H, 5 interactions with chain F, 1 Ligand-Ligand interactions Hydrogen bonds: H:H.76, F:L.96, F:A.130, H.8 Salt bridges: H:H.76, F:R.87, F:R.97, F:H.137 pi-Stacking: H:Y.75 HIS.9: 11 residues within 4Å: Chain F: Y.68, H.72, Y.75, H.76 Chain G: R.87, R.97, I.128, G.129, A.130, H.137 Ligands: MG.7 9 PLIP interactions: 3 interactions with chain F, 5 interactions with chain G, 1 Ligand-Ligand interactions Hydrogen bonds: F:H.76, G:L.96, G:A.130, H.9 Salt bridges: F:H.76, G:R.87, G:R.97, G:H.137 pi-Stacking: F:Y.75 HIS.10: 11 residues within 4Å: Chain G: Y.68, H.72, Y.75, H.76 Chain H: R.87, R.97, I.128, G.129, A.130, H.137 Ligands: MG.11 9 PLIP interactions: 5 interactions with chain H, 1 Ligand-Ligand interactions, 3 interactions with chain G Hydrogen bonds: H:L.96, H:A.130, H.10, G:Y.68, G:H.76 Salt bridges: H:R.87, H:R.97, H:H.137, G:H.76

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kumarevel, T. et al., Crystal Structure of HutP complexed with the 55-mer RNA. To be Published

Release Date

2008-01-15

Peptides

Hut operon positive regulatory protein: BCDFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
A

C
B

D
C

F
A

G
B

H
C

Hut operon positive regulatory protein

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