SMTL ID : 7p52.1

GlnK1 from Methanocaldococcus jannaschii with Mg-ATP and 2-oxoglutarate at a resolution of 1.2 A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.20 Å

Oligo State

homo-trimer

Ligands

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

ATP.1: 24 residues within 4Å: Chain A: I.7, G.35, R.36, G.37, V.38, Q.39, K.58, P.86, G.87, D.88, G.89, K.90, F.92 Chain B: G.27, M.28, T.29, E.62, L.63, V.64, R.101, R.103, L.112 Ligands: AKG.2, MG.5 18 PLIP interactions: 8 interactions with chain B, 10 interactions with chain A Hydrogen bonds: B:V.64, B:V.64, B:L.112, A:V.38, A:Q.39, A:G.87, A:G.89 Water bridges: B:V.102, B:R.103, A:G.37, A:G.37, A:K.90 Salt bridges: B:R.101, B:R.101, B:R.103, A:K.90, A:K.90 pi-Stacking: A:F.92 ATP.6: 24 residues within 4Å: Chain B: I.7, G.35, R.36, G.37, V.38, Q.39, K.58, P.86, G.87, D.88, G.89, K.90, F.92 Chain C: G.27, M.28, T.29, E.62, L.63, V.64, R.101, R.103, L.112 Ligands: AKG.7, MG.10 18 PLIP interactions: 10 interactions with chain B, 8 interactions with chain C Hydrogen bonds: B:V.38, B:Q.39, B:G.87, B:G.89, C:V.64, C:V.64, C:L.112 Water bridges: B:G.37, B:G.37, B:K.90, C:V.102, C:R.103 Salt bridges: B:K.90, B:K.90, C:R.101, C:R.101, C:R.103 pi-Stacking: B:F.92 ATP.11: 24 residues within 4Å: Chain A: G.27, M.28, T.29, E.62, L.63, V.64, R.101, R.103, L.112 Chain C: I.7, G.35, R.36, G.37, V.38, Q.39, K.58, P.86, G.87, D.88, G.89, K.90, F.92 Ligands: AKG.12, MG.15 18 PLIP interactions: 8 interactions with chain A, 10 interactions with chain C Hydrogen bonds: A:V.64, A:V.64, A:L.112, C:V.38, C:Q.39, C:G.87, C:G.89 Water bridges: A:V.102, A:R.103, C:G.37, C:G.37, C:K.90 Salt bridges: A:R.101, A:R.101, A:R.103, 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, R.36, G.37, V.38, Q.39, G.40, G.41, I.42, I.56, K.58, P.86, G.87 Ligands: ATP.1, MG.5 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.42 Hydrogen bonds: A:G.37, A:Q.39, A:G.40, A:G.41 Water bridges: A:R.9 Salt bridges: A:R.9, A:K.58 AKG.7: 14 residues within 4Å: Chain B: R.9, R.36, G.37, V.38, Q.39, G.40, G.41, I.42, I.56, K.58, P.86, G.87 Ligands: ATP.6, MG.10 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:I.42 Hydrogen bonds: B:G.37, B:Q.39, B:G.40, B:G.41 Water bridges: B:R.9 Salt bridges: B:R.9, B:K.58 AKG.12: 14 residues within 4Å: Chain C: R.9, R.36, G.37, V.38, Q.39, G.40, G.41, I.42, I.56, K.58, P.86, G.87 Ligands: ATP.11, MG.15 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:I.42 Hydrogen bonds: C:G.37, C:Q.39, C:G.40, C:G.41 Water bridges: C:R.9 Salt bridges: C:R.9, C:K.58

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: G.24, Y.25, V.26, G.27, V.65, L.112 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.24, A:V.26, A:G.27, A:L.112 Water bridges: A:K.66, A:K.66, A:K.66 GOL.8: 6 residues within 4Å: Chain B: G.24, Y.25, V.26, G.27, V.65, L.112 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.24, B:V.26, B:G.27, B:L.112 Water bridges: B:K.66, B:K.66, B:K.66 GOL.13: 6 residues within 4Å: Chain C: G.24, Y.25, V.26, G.27, V.65, L.112 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:G.24, C:V.26, C:G.27, C:L.112 Water bridges: C:K.66, C:K.66, C:K.66

3 x NO3: NITRATE ION(Non-functional Binders)

NO3.4: 8 residues within 4Å: Chain A: K.3, I.94 Chain B: K.3, I.94 Chain C: K.3, I.94 Ligands: NO3.9, NO3.14 8 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B, 2 interactions with chain C Hydrogen bonds: A:K.3, B:E.5 Water bridges: A:K.3, A:K.3, B:K.3, B:K.3, C:K.3, C:K.3 NO3.9: 8 residues within 4Å: Chain A: K.3, I.94 Chain B: K.3, I.94 Chain C: K.3, I.94 Ligands: NO3.4, NO3.14 8 PLIP interactions: 2 interactions with chain A, 3 interactions with chain C, 3 interactions with chain B Water bridges: A:K.3, A:K.3, C:K.3, C:K.3, B:K.3, B:K.3 Hydrogen bonds: C:E.5, B:K.3 NO3.14: 8 residues within 4Å: Chain A: K.3, I.94 Chain B: K.3, I.94 Chain C: K.3, I.94 Ligands: NO3.4, NO3.9 8 PLIP interactions: 3 interactions with chain A, 3 interactions with chain C, 2 interactions with chain B Hydrogen bonds: A:E.5, C:K.3 Water bridges: A:K.3, A:K.3, C:K.3, C:K.3, B:K.3, B:K.3

3 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 4 residues within 4Å: Chain A: Q.39, G.87 Ligands: ATP.1, AKG.2 No protein-ligand interaction detected (PLIP) MG.10: 4 residues within 4Å: Chain B: Q.39, G.87 Ligands: ATP.6, AKG.7 No protein-ligand interaction detected (PLIP) MG.15: 4 residues within 4Å: Chain C: Q.39, G.87 Ligands: ATP.11, AKG.12 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Muller, M.C. et al., The Oxoglutarate Binding Site and Regulatory Mechanism Are Conserved in Ammonium Transporter Inhibitors GlnKs from Methanococcales . Int J Mol Sci (2021)

Release Date

2021-10-06

Peptides

Nitrogen regulatory protein GlnK1: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Nitrogen regulatory protein GlnK1