SMTL ID : 1wpv.1

Crystal Structure of Activated Binary complex of HutP, an RNA binding anti-termination protein

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 A: H.72, H.76 Chain B: H.137 Ligands: HIS.3 5 PLIP interactions: 1 Ligand-Ligand interactions, 2 interactions with chain A, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: HIS.3, A:H.72, A:H.76, B:H.137, H2O.1 MG.4: 4 residues within 4Å: Chain B: H.72, H.76 Chain C: H.137 Ligands: HIS.6 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.6, C:H.137, H2O.8 MG.5: 4 residues within 4Å: Chain A: H.137 Chain C: H.72, H.76 Ligands: HIS.2 5 PLIP interactions: 2 interactions with chain C, 1 Ligand-Ligand interactions, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: C:H.72, C:H.76, HIS.2, A:H.137, H2O.15 MG.7: 4 residues within 4Å: Chain D: H.72, H.76 Chain E: H.137 Ligands: HIS.9 5 PLIP interactions: 1 Ligand-Ligand interactions, 2 interactions with chain D, 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: HIS.9, D:H.72, D:H.76, E:H.137, H2O.23 MG.10: 4 residues within 4Å: Chain E: H.72, H.76 Chain F: H.137 Ligands: HIS.12 5 PLIP interactions: 2 interactions with chain E, 1 Ligand-Ligand interactions, 1 interactions with chain F, 1 Ligand-Water interactions Metal complexes: E:H.72, E:H.76, HIS.12, F:H.137, H2O.30 MG.11: 4 residues within 4Å: Chain D: H.137 Chain F: H.72, H.76 Ligands: HIS.8 5 PLIP interactions: 1 Ligand-Ligand interactions, 1 interactions with chain D, 2 interactions with chain F, 1 Ligand-Water interactions Metal complexes: HIS.8, D:H.137, F:H.72, F:H.76, H2O.37

6 x HIS: HISTIDINE(Non-covalent)

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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kumarevel, T. et al., Structural basis of HutP-mediated anti-termination and roles of the Mg2+ ion and L-histidine ligand. Nature (2005)

Release Date

2005-03-15

Peptides

Hut operon positive regulatory protein: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

Hut operon positive regulatory protein

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