SMTL ID : 4aff.1

High resolution structure of a PII mutant (I86N) protein in complex with ATP, MG and FLC

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.05 Å

Oligo State

homo-trimer

Ligands

3 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 22 residues within 4Å: Chain A: I.7, G.35, F.36, G.37, R.38, K.58, N.86, G.87, D.88, G.89, K.90, F.92 Chain C: G.27, M.28, T.29, E.62, I.63, V.64, R.101, R.103 Ligands: MG.2, FLC.3 21 PLIP interactions: 6 interactions with chain C, 15 interactions with chain A Hydrogen bonds: C:V.64, C:V.64, A:G.35, A:R.38, A:G.87, A:G.89 Water bridges: C:I.102, A:G.37, A:G.37, A:R.38, A:R.38, A:D.88, A:K.90, A:K.90 Salt bridges: C:R.101, C:R.101, C:R.103, A:R.38, A:R.38, A:K.90, A:K.90 ATP.4: 22 residues within 4Å: Chain A: G.27, M.28, T.29, E.62, I.63, V.64, R.101, R.103 Chain B: I.7, G.35, F.36, G.37, R.38, K.58, N.86, G.87, D.88, G.89, K.90, F.92 Ligands: MG.5, FLC.6 21 PLIP interactions: 15 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:G.35, B:R.38, B:G.87, B:G.89, A:V.64, A:V.64 Water bridges: B:G.37, B:G.37, B:R.38, B:R.38, B:D.88, B:K.90, B:K.90, A:I.102 Salt bridges: B:R.38, B:R.38, B:K.90, B:K.90, A:R.101, A:R.101, A:R.103 ATP.7: 22 residues within 4Å: Chain B: G.27, M.28, T.29, E.62, I.63, V.64, R.101, R.103 Chain C: I.7, G.35, F.36, G.37, R.38, K.58, N.86, G.87, D.88, G.89, K.90, F.92 Ligands: MG.8, FLC.9 21 PLIP interactions: 15 interactions with chain C, 6 interactions with chain B Hydrogen bonds: C:G.35, C:R.38, C:G.87, C:G.89, B:V.64, B:V.64 Water bridges: C:G.37, C:G.37, C:R.38, C:R.38, C:D.88, C:K.90, C:K.90, B:I.102 Salt bridges: C:R.38, C:R.38, C:K.90, C:K.90, B:R.101, B:R.101, B:R.103

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: G.87 Ligands: ATP.1, FLC.3 No protein-ligand interaction detected (PLIP) MG.5: 3 residues within 4Å: Chain B: G.87 Ligands: ATP.4, FLC.6 No protein-ligand interaction detected (PLIP) MG.8: 3 residues within 4Å: Chain C: G.87 Ligands: ATP.7, FLC.9 No protein-ligand interaction detected (PLIP)

3 x FLC: CITRATE ANION(Non-covalent)

FLC.3: 10 residues within 4Å: Chain A: F.36, G.37, R.38, Q.39, K.40, L.56, N.86, G.87 Ligands: ATP.1, MG.2 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:N.86 Hydrogen bonds: A:G.37, A:Q.39, A:K.40 Water bridges: A:R.9, A:R.9 Salt bridges: A:K.58 FLC.6: 10 residues within 4Å: Chain B: F.36, G.37, R.38, Q.39, K.40, L.56, N.86, G.87 Ligands: ATP.4, MG.5 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:N.86 Hydrogen bonds: B:G.37, B:Q.39, B:K.40 Water bridges: B:R.9, B:R.9 Salt bridges: B:K.58 FLC.9: 10 residues within 4Å: Chain C: F.36, G.37, R.38, Q.39, K.40, L.56, N.86, G.87 Ligands: ATP.7, MG.8 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:N.86 Hydrogen bonds: C:G.37, C:Q.39, C:K.40 Water bridges: C:R.9, C:R.9 Salt bridges: C:K.58

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zeth, K. et al., An Engineered Pii Protein Variant that Senses a Novel Ligand: Atomic Resolution Structure of the Complex with Citrate. Acta Crystallogr.,Sect.D (2012)

Release Date

2012-02-01

Peptides

NITROGEN REGULATORY PROTEIN P-II: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

NITROGEN REGULATORY PROTEIN P-II