SMTL ID : 4h4l.1 (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, I.129, G.130, A.131, H.138 Ligands: ZN.2 9 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A, 2 Ligand-Ligand interactions Hydrophobic interactions: B:R.98, A:Y.76 Hydrogen bonds: B:R.88, B:L.97, B:R.98, B:A.131, A:Y.69, H.1 Salt bridges: H.1 HIS.3: 13 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, L.136, H.138 Ligands: ZN.4 9 PLIP interactions: 5 interactions with chain C, 1 Ligand-Ligand interactions, 3 interactions with chain B Hydrophobic interactions: C:R.98, B:Y.76 Hydrogen bonds: C:R.88, C:R.88, C:R.98, C:A.131, B:Y.69, B:Y.76 Salt bridges: H.3 HIS.5: 12 residues within 4Å: Chain A: R.88, L.97, R.98, I.129, G.130, A.131, H.138 Chain C: Y.69, H.73, Y.76, H.77 Ligands: ZN.6 6 PLIP interactions: 2 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.98, C:Y.69, C:Y.76 Salt bridges: H.5 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 7 PLIP interactions: 1 Ligand-Ligand interactions, 5 interactions with chain E, 1 interactions with chain D Salt bridges: H.7 Hydrophobic interactions: E:R.98, D:Y.76 Hydrogen bonds: E:R.88, E:R.88, E:R.98, E:A.131 HIS.9: 12 residues within 4Å: Chain D: R.88, L.97, R.98, I.129, G.130, A.131, H.138 Chain F: Y.69, H.73, Y.76, H.77 Ligands: ZN.12 8 PLIP interactions: 6 interactions with chain D, 1 interactions with chain F, 1 Ligand-Ligand interactions Hydrophobic interactions: D:R.98, D:I.129 Hydrogen bonds: D:R.88, D:R.88, D:L.97, D:R.98, F:Y.69 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, 1 Ligand-Ligand interactions, 2 interactions with chain E 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: 1 Ligand-Ligand interactions, 2 interactions with chain A, 1 interactions with chain B Metal complexes: HIS.1, A:H.73, A:H.77, B:H.138 ZN.4: 4 residues within 4Å: Chain B: H.73, H.77 Chain C: H.138 Ligands: HIS.3 4 PLIP interactions: 2 interactions with chain B, 1 Ligand-Ligand interactions, 1 interactions with chain C Metal complexes: B:H.73, B:H.77, HIS.3, C:H.138 ZN.6: 4 residues within 4Å: Chain A: H.138 Chain C: H.73, H.77 Ligands: HIS.5 4 PLIP interactions: 2 interactions with chain C, 1 Ligand-Ligand interactions, 1 interactions with chain A Metal complexes: C:H.73, C:H.77, HIS.5, A:H.138 ZN.8: 5 residues within 4Å: Chain D: H.73, H.77 Chain E: R.88, H.138 Ligands: HIS.7 4 PLIP interactions: 1 Ligand-Ligand interactions, 2 interactions with chain D, 1 interactions with chain E Metal complexes: HIS.7, D:H.73, D:H.77, E:H.138 ZN.10: 4 residues within 4Å: Chain E: H.73, H.77 Chain F: H.138 Ligands: HIS.11 4 PLIP interactions: 1 Ligand-Ligand interactions, 2 interactions with chain E, 1 interactions with chain F Metal complexes: HIS.11, E:H.73, E:H.77, F:H.138 ZN.12: 4 residues within 4Å: Chain D: H.138 Chain F: H.73, H.77 Ligands: HIS.9 4 PLIP interactions: 1 interactions with chain D, 2 interactions with chain F, 1 Ligand-Ligand interactions Metal complexes: D:H.138, F:H.73, F:H.77, HIS.9

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
A

B
B

C
C

D
J

E
K

F
L

Hut operon positive regulatory protein

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