SMTL ID : 3mhy.1

A New PII Protein Structure

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-trimer

Ligands

3 x PG6: 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE(Non-covalent)

PG6.1: 8 residues within 4Å: Chain A: V.33, K.34, F.55, P.57 Chain C: L.13, V.30, S.31, E.32 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.34 PG6.10: 8 residues within 4Å: Chain A: L.13, V.30, S.31, E.32 Chain B: E.32, V.33, K.34, F.55 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.34 Water bridges: B:F.55, B:F.55, B:F.55, A:E.32 PG6.11: 4 residues within 4Å: Chain B: L.13, V.30, S.31 Chain C: K.34 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:E.32, C:K.34, C:K.34 Water bridges: C:E.32

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

ATP.2: 24 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 C: G.27, L.28, T.29, E.62, V.63, A.64, R.101, R.103, L.112 Ligands: AKG.3, MG.4 19 PLIP interactions: 12 interactions with chain A, 7 interactions with chain C Hydrogen bonds: A:R.38, A:G.87, A:G.89, C:T.29, C:A.64, C:A.64, C:L.112 Water bridges: A:K.58, A:K.58, A:D.88, A:K.90, C:I.102 Salt bridges: A:R.38, A:R.38, A:K.90, A:K.90, C:R.101, C:R.103 pi-Stacking: A:F.92 ATP.6: 24 residues within 4Å: Chain A: G.27, L.28, T.29, E.62, V.63, A.64, R.101, R.103, L.112 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 Ligands: AKG.7, MG.8 21 PLIP interactions: 8 interactions with chain A, 13 interactions with chain B Hydrogen bonds: A:T.29, A:A.64, A:A.64, B:R.38, B:Q.39, B:Q.39, B:G.87, B:G.89 Water bridges: A:R.101, A:I.102, B:K.58, B:K.58, B:D.88 Salt bridges: A:R.101, A:R.101, A:R.103, B:R.38, B:R.38, B:K.90, B:K.90 pi-Stacking: B:F.92 ATP.12: 24 residues within 4Å: Chain B: G.27, L.28, T.29, E.62, V.63, A.64, R.101, R.103, L.112 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.13, MG.14 24 PLIP interactions: 15 interactions with chain C, 9 interactions with chain B Hydrogen bonds: C:R.38, C:Q.39, C:Q.39, C:G.87, C:G.89, B:A.64, B:A.64 Water bridges: C:K.58, C:K.58, C:D.88, C:K.90, B:Q.26, B:Q.26, B:G.27, 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 pi-Stacking: C:F.92, C:F.92

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

AKG.3: 14 residues within 4Å: Chain A: K.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.2, MG.4 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.56, A:I.86 Hydrogen bonds: A:G.37, A:Q.39, A:Q.39, A:K.40, A:G.41 Water bridges: A:K.58, A:K.58, A:K.58 Salt bridges: A:K.9, A:K.58 AKG.7: 13 residues within 4Å: Chain B: K.9, F.36, G.37, R.38, Q.39, K.40, G.41, L.56, K.58, I.86, G.87 Ligands: ATP.6, MG.8 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:L.56, B:I.86 Hydrogen bonds: B:G.37, B:Q.39, B:K.40, B:G.41 Water bridges: B:K.9, B:K.58, B:K.58, B:K.58, B:K.58 Salt bridges: B:K.9, B:K.58 AKG.13: 14 residues within 4Å: Chain C: K.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.12, MG.14 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:L.56, C:I.86 Hydrogen bonds: C:G.37, C:Q.39, C:K.40, C:G.41 Water bridges: C:K.58, C:K.58, C:K.58 Salt bridges: C:K.9, C:K.58

4 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.4: 5 residues within 4Å: Chain A: R.38, Q.39, G.87 Ligands: ATP.2, AKG.3 No protein-ligand interaction detected (PLIP) MG.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.8: 4 residues within 4Å: Chain B: Q.39, G.87 Ligands: ATP.6, AKG.7 No protein-ligand interaction detected (PLIP) MG.14: 5 residues within 4Å: Chain C: R.38, Q.39, G.87 Ligands: ATP.12, AKG.13 No protein-ligand interaction detected (PLIP)

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.9: 4 residues within 4Å: Chain B: S.66, D.67, D.68, T.109 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.67, B:D.68 Water bridges: B:S.66, B:S.66 Salt bridges: B:D.68

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Truan, D. et al., A new P(II) protein structure identifies the 2-oxoglutarate binding site. J.Mol.Biol. (2010)

Release Date

2010-06-09

Peptides

PII-like protein Pz: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

PII-like protein Pz

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