SMTL ID : 2xul.1 (1 other biounit)

STRUCTURE OF PII FROM SYNECHOCOCCUS ELONGATUS IN COMPLEX WITH 2-OXOGLUTARATE AT HIGH 2-OG CONCENTRATIONS

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-trimer

Ligands

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

ATP.1: 23 residues within 4Å: Chain A: I.7, G.35, F.36, G.37, R.38, Q.39, K.58, I.86, G.87, D.88, G.89, K.90, F.92 Chain B: G.27, M.28, T.29, E.62, I.63, V.64, R.101, R.103 Ligands: AKG.2, MG.3 18 PLIP interactions: 13 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:R.38, A:Q.39, A:G.87, A:G.89, B:V.64, B:V.64 Water bridges: A:G.37, A:K.58, A:D.88, A:D.88, A:K.90, A:K.90 Salt bridges: A:R.38, A:K.90, A:K.90, B:R.101, B:R.101, B:R.103 ATP.4: 23 residues within 4Å: Chain B: I.7, G.35, F.36, G.37, R.38, Q.39, K.58, I.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: AKG.5, MG.6 20 PLIP interactions: 14 interactions with chain B, 6 interactions with chain C Hydrogen bonds: B:G.37, B:R.38, B:Q.39, B:G.87, B:G.89, C:T.29, C:V.64, C:V.64 Water bridges: B:K.58, B:K.58, B:D.88, B:D.88 Salt bridges: B:R.38, B:R.38, B:K.90, B:K.90, C:R.101, C:R.101, C:R.103 pi-Stacking: B:F.92 ATP.7: 23 residues within 4Å: Chain A: 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, Q.39, K.58, I.86, G.87, D.88, G.89, K.90, F.92 Ligands: AKG.8, MG.9 21 PLIP interactions: 5 interactions with chain A, 16 interactions with chain C Hydrogen bonds: A:V.64, A:V.64, C:R.38, C:Q.39, C:Q.39, C:G.87, C:G.89 Salt bridges: A:R.101, A:R.101, A:R.103, C:R.38, C:R.38, C:K.90, C:K.90 Water bridges: C:G.37, C:K.58, C:D.88, C:D.88, C:K.90, C:K.90 pi-Stacking: C:F.92

3 x AKG: 2-OXOGLUTARIC ACID(Non-covalent)

AKG.2: 14 residues within 4Å: Chain A: R.9, F.36, G.37, R.38, Q.39, K.40, G.41, Q.42, L.56, K.58, I.86, G.87 Ligands: ATP.1, MG.3 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.56 Hydrogen bonds: A:G.37, A:Q.39, A:Q.39, A:G.41 Water bridges: A:K.58, A:K.58 Salt bridges: A:R.9, A:K.58 AKG.5: 14 residues within 4Å: Chain B: R.9, F.36, G.37, R.38, Q.39, K.40, G.41, Q.42, L.56, K.58, I.86, G.87 Ligands: ATP.4, MG.6 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:L.56 Hydrogen bonds: B:G.37, B:Q.39, B:Q.39, B:K.40, B:G.41 Water bridges: B:R.9, B:K.58, B:K.58, B:K.58 Salt bridges: B:R.9, B:K.58 AKG.8: 15 residues within 4Å: Chain C: R.9, F.36, G.37, R.38, Q.39, K.40, G.41, Q.42, T.43, L.56, K.58, I.86, G.87 Ligands: ATP.7, MG.9 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:T.43, C:L.56 Hydrogen bonds: C:G.37, C:Q.39, C:K.40, C:G.41 Water bridges: C:K.58, C:K.58 Salt bridges: C:R.9, C:K.58

3 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: Q.39, G.87 Ligands: ATP.1, AKG.2 No protein-ligand interaction detected (PLIP) MG.6: 5 residues within 4Å: Chain B: R.38, Q.39, G.87 Ligands: ATP.4, AKG.5 No protein-ligand interaction detected (PLIP) MG.9: 5 residues within 4Å: Chain C: R.38, Q.39, G.87 Ligands: ATP.7, AKG.8 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fokina, O. et al., Mechanism of 2-Oxoglutarate Signaling by the Synechococcus Elongatus Pii Signal Transduction Protein. Proc.Natl.Acad.Sci.USA (2010)

Release Date

2010-11-03

Peptides

NITROGEN REGULATORY PROTEIN P-II: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

NITROGEN REGULATORY PROTEIN P-II

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