SMTL ID : 4h4l.2 (1 other biounit)

Crystal Structure of ternary complex of HutP(HutP-L-His-Zn)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-hexamer

Ligands

6 x HIS: HISTIDINE(Non-covalent)

HIS.1: 12 residues within 4Å: Chain A: Y.69, H.73, Y.76, H.77 Chain B: R.88, L.97, R.98, G.130, A.131, L.136, H.138 Ligands: ZN.2 8 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B, 2 Ligand-Ligand interactions Hydrophobic interactions: A:Y.76, B:R.98 Hydrogen bonds: A:Y.69, B:L.97, B:R.98, B:A.131, H.1 Salt bridges: H.1 HIS.3: 13 residues within 4Å: Chain A: R.88, L.97, R.98, I.129, G.130, A.131, L.136, H.138 Chain C: Y.69, H.73, Y.76, H.77 Ligands: ZN.6 7 PLIP interactions: 3 interactions with chain A, 3 interactions with chain C, 1 Ligand-Ligand interactions Hydrophobic interactions: A:R.98, C:Y.76 Hydrogen bonds: A:R.88, A:R.98, C:Y.69, C:Y.76 Salt bridges: H.3 HIS.5: 12 residues within 4Å: Chain B: Y.69, H.73, Y.76, H.77 Chain C: R.88, L.97, R.98, I.129, G.130, A.131, H.138 Ligands: ZN.4 7 PLIP interactions: 2 interactions with chain B, 1 Ligand-Ligand interactions, 4 interactions with chain C Hydrogen bonds: B:Y.69, B:Y.76, C:R.88, C:R.88, C:R.98 Salt bridges: H.5 Hydrophobic interactions: C:R.98 HIS.7: 11 residues within 4Å: Chain D: Y.69, H.73, Y.76, H.77 Chain E: R.88, L.97, R.98, G.130, A.131, H.138 Ligands: ZN.8 6 PLIP interactions: 3 interactions with chain E, 2 interactions with chain D, 1 Ligand-Ligand interactions Hydrogen bonds: E:R.88, E:R.88, E:A.131, D:Y.69, D:Y.76, H.7 HIS.9: 11 residues within 4Å: Chain D: R.88, L.97, R.98, I.129, G.130, H.138 Chain F: Y.69, H.73, Y.76, H.77 Ligands: ZN.12 6 PLIP interactions: 2 interactions with chain F, 1 Ligand-Ligand interactions, 3 interactions with chain D Hydrogen bonds: F:Y.69, F:Y.76, D:R.88, D:R.88, D:R.98 Salt bridges: H.9 HIS.11: 12 residues within 4Å: Chain E: Y.69, H.73, Y.76, H.77 Chain F: R.88, L.97, R.98, I.129, G.130, A.131, H.138 Ligands: ZN.10 8 PLIP interactions: 5 interactions with chain F, 2 interactions with chain E, 1 Ligand-Ligand interactions Hydrophobic interactions: F:R.98 Hydrogen bonds: F:R.88, F:R.88, F:R.98, F:A.131, E:Y.69, E:Y.76 Salt bridges: H.11

6 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: H.73, H.77 Chain B: H.138 Ligands: HIS.1 4 PLIP interactions: 2 interactions with chain A, 1 Ligand-Ligand interactions, 1 interactions with chain B Metal complexes: A:H.73, A:H.77, HIS.1, B:H.138 ZN.4: 4 residues within 4Å: Chain B: H.73, H.77 Chain C: H.138 Ligands: HIS.5 4 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: C:H.138, B:H.73, B:H.77, HIS.5 ZN.6: 4 residues within 4Å: Chain A: H.138 Chain C: H.73, H.77 Ligands: HIS.3 5 PLIP interactions: 1 Ligand-Ligand interactions, 1 interactions with chain A, 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: HIS.3, A:H.138, C:H.73, C:H.77, H2O.2 ZN.8: 4 residues within 4Å: Chain D: H.73, H.77 Chain E: H.138 Ligands: HIS.7 4 PLIP interactions: 1 interactions with chain E, 1 Ligand-Ligand interactions, 2 interactions with chain D Metal complexes: E:H.138, HIS.7, D:H.73, D:H.77 ZN.10: 4 residues within 4Å: Chain E: H.73, H.77 Chain F: H.138 Ligands: HIS.11 4 PLIP interactions: 2 interactions with chain E, 1 interactions with chain F, 1 Ligand-Ligand interactions Metal complexes: E:H.73, E:H.77, F:H.138, HIS.11 ZN.12: 4 residues within 4Å: Chain D: H.138 Chain F: H.73, H.77 Ligands: HIS.9 4 PLIP interactions: 2 interactions with chain F, 1 Ligand-Ligand interactions, 1 interactions with chain D Metal complexes: F:H.73, F:H.77, HIS.9, D:H.138

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dhakshnamoorthy, B. et al., Alternative binding modes of l-histidine guided by metal ions for the activation of the antiterminator protein HutP of Bacillus subtilis. J.Struct.Biol. (2013)

Release Date

2013-09-04

Peptides

Hut operon positive regulatory protein: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

C
F

D
G

E
H

F
I

Hut operon positive regulatory protein

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