SMTL ID : 4okq.1

Crystal structure of the single-stranded RNA binding protein HutP from Geobacillus thermodenitrificans

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-hexamer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: H.74, H.78 Chain C: H.139 Ligands: HIS.2 5 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: C:H.139, A:H.74, A:H.78, HIS.2, H2O.2 MG.3: 4 residues within 4Å: Chain B: H.74, H.78 Chain F: H.139 Ligands: HIS.4 4 PLIP interactions: 2 interactions with chain B, 1 interactions with chain F, 1 Ligand-Water interactions Metal complexes: B:H.74, B:H.78, F:H.139, H2O.3 MG.5: 4 residues within 4Å: Chain C: H.74, H.78 Chain E: H.139 Ligands: HIS.6 5 PLIP interactions: 1 Ligand-Ligand interactions, 1 interactions with chain E, 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: HIS.6, E:H.139, C:H.74, C:H.78, H2O.4 MG.7: 4 residues within 4Å: Chain B: H.139 Chain D: H.74, H.78 Ligands: HIS.8 4 PLIP interactions: 1 interactions with chain B, 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: B:H.139, D:H.74, D:H.78, H2O.5 MG.9: 4 residues within 4Å: Chain A: H.139 Chain E: H.74, H.78 Ligands: HIS.10 5 PLIP interactions: 2 interactions with chain E, 1 Ligand-Ligand interactions, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: E:H.74, E:H.78, HIS.10, A:H.139, H2O.6 MG.11: 4 residues within 4Å: Chain D: H.139 Chain F: H.74, H.78 Ligands: HIS.12 4 PLIP interactions: 1 interactions with chain D, 2 interactions with chain F, 1 Ligand-Water interactions Metal complexes: D:H.139, F:H.74, F:H.78, H2O.8

6 x HIS: HISTIDINE(Non-covalent)

HIS.2: 12 residues within 4Å: Chain A: Y.70, H.74, Y.77, H.78 Chain C: R.89, L.98, R.99, I.130, G.131, A.132, H.139 Ligands: MG.1 9 PLIP interactions: 4 interactions with chain C, 3 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: C:L.98, H.2, H.2 Salt bridges: C:R.89, C:R.99, C:H.139, A:H.78 Hydrophobic interactions: A:Y.77 pi-Stacking: A:Y.77 HIS.4: 12 residues within 4Å: Chain B: Y.70, H.74, Y.77, H.78 Chain F: R.89, L.98, R.99, I.130, G.131, A.132, H.139 Ligands: MG.3 12 PLIP interactions: 5 interactions with chain F, 3 interactions with chain B, 4 Ligand-Ligand interactions Hydrogen bonds: F:L.98, F:A.132, B:Y.70, H.4, H.4, H.4, H.4 Salt bridges: F:R.89, F:R.99, F:H.139, B:H.78 pi-Stacking: B:Y.77 HIS.6: 12 residues within 4Å: Chain C: Y.70, H.74, Y.77, H.78 Chain E: R.89, L.98, R.99, I.130, G.131, A.132, H.139 Ligands: MG.5 9 PLIP interactions: 4 interactions with chain E, 2 Ligand-Ligand interactions, 3 interactions with chain C Hydrogen bonds: E:L.98, H.6, H.6 Salt bridges: E:R.89, E:R.99, E:H.139, C:H.78 Hydrophobic interactions: C:Y.77 pi-Stacking: C:Y.77 HIS.8: 12 residues within 4Å: Chain B: R.89, L.98, R.99, I.130, G.131, A.132, H.139 Chain D: Y.70, H.74, Y.77, H.78 Ligands: MG.7 12 PLIP interactions: 5 interactions with chain B, 3 interactions with chain D, 4 Ligand-Ligand interactions Hydrogen bonds: B:L.98, B:A.132, D:Y.70, H.8, H.8, H.8, H.8 Salt bridges: B:R.89, B:R.99, B:H.139, D:H.78 pi-Stacking: D:Y.77 HIS.10: 12 residues within 4Å: Chain A: R.89, L.98, R.99, I.130, G.131, A.132, H.139 Chain E: Y.70, H.74, Y.77, H.78 Ligands: MG.9 9 PLIP interactions: 4 interactions with chain A, 3 interactions with chain E, 2 Ligand-Ligand interactions Hydrogen bonds: A:L.98, H.10, H.10 Salt bridges: A:R.89, A:R.99, A:H.139, E:H.78 Hydrophobic interactions: E:Y.77 pi-Stacking: E:Y.77 HIS.12: 12 residues within 4Å: Chain D: R.89, L.98, R.99, I.130, G.131, A.132, H.139 Chain F: Y.70, H.74, Y.77, H.78 Ligands: MG.11 12 PLIP interactions: 5 interactions with chain D, 4 Ligand-Ligand interactions, 3 interactions with chain F Hydrogen bonds: D:L.98, D:A.132, H.12, H.12, H.12, H.12, F:Y.70 Salt bridges: D:R.89, D:R.99, D:H.139, F:H.78 pi-Stacking: F:Y.77

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thiruselvam, V. et al., Crystal structure of the single-stranded RNA binding protein HutP from Geobacillus thermodenitrificans. Biochem.Biophys.Res.Commun. (2014)

Release Date

2014-03-19

Peptides

Hut operon positive regulatory protein: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

Hut operon positive regulatory protein

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