SMTL ID : 7p50.1

GlnK2 from Methanothermococcus thermolithotrophicus in complex with Mg-ATP and 2-oxoglutarate at a resolution of 1.16 A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.16 Å

Oligo State

homo-trimer

Ligands

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

AKG.1: 14 residues within 4Å: Chain A: R.29, R.56, G.57, I.58, Q.59, G.60, G.61, I.62, L.76, K.78, Q.106, G.107 Ligands: MG.2, ATP.3 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:I.62, A:L.76 Hydrogen bonds: A:G.57, A:Q.59, A:G.60, A:G.61, A:G.61 Water bridges: A:R.29, A:K.78, A:Q.106 Salt bridges: A:R.29, A:K.78 AKG.4: 14 residues within 4Å: Chain B: R.29, R.56, G.57, I.58, Q.59, G.60, G.61, I.62, L.76, K.78, Q.106, G.107 Ligands: MG.5, ATP.6 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:I.62 Hydrogen bonds: B:G.57, B:Q.59, B:G.60, B:G.61, B:G.61 Water bridges: B:K.78 Salt bridges: B:R.29, B:K.78 AKG.7: 14 residues within 4Å: Chain C: R.29, R.56, G.57, I.58, Q.59, G.60, G.61, I.62, L.76, K.78, Q.106, G.107 Ligands: MG.11, ATP.12 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:I.62, C:L.76 Hydrogen bonds: C:G.57, C:Q.59, C:G.60, C:G.61, C:G.61 Water bridges: C:R.29, C:K.78, C:Q.106 Salt bridges: C:R.29, C:K.78

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: Q.59, G.107 Ligands: AKG.1, ATP.3 No protein-ligand interaction detected (PLIP) MG.5: 4 residues within 4Å: Chain B: Q.59, G.107 Ligands: AKG.4, ATP.6 No protein-ligand interaction detected (PLIP) MG.11: 4 residues within 4Å: Chain C: Q.59, G.107 Ligands: AKG.7, ATP.12 No protein-ligand interaction detected (PLIP)

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

ATP.3: 24 residues within 4Å: Chain A: I.27, G.55, R.56, G.57, I.58, Q.59, K.78, Q.106, G.107, D.108, G.109, K.110, F.112 Chain B: G.47, M.48, T.49, E.82, L.83, V.84, R.121, R.123, I.132 Ligands: AKG.1, MG.2 21 PLIP interactions: 9 interactions with chain B, 12 interactions with chain A Hydrogen bonds: B:T.49, B:V.84, B:V.84, B:I.132, A:G.57, A:I.58, A:Q.59, A:Q.59, A:G.107, A:G.109 Water bridges: B:V.122, B:R.123, A:K.78, A:K.78, A:D.108 Salt bridges: B:R.121, B:R.121, B:R.123, A:K.110, A:K.110 pi-Stacking: A:F.112 ATP.6: 24 residues within 4Å: Chain B: I.27, G.55, R.56, G.57, I.58, Q.59, K.78, Q.106, G.107, D.108, G.109, K.110, F.112 Chain C: G.47, M.48, T.49, E.82, L.83, V.84, R.121, R.123, I.132 Ligands: AKG.4, MG.5 22 PLIP interactions: 12 interactions with chain B, 10 interactions with chain C Hydrogen bonds: B:G.57, B:I.58, B:Q.59, B:Q.59, B:G.107, B:G.109, C:T.49, C:V.84, C:V.84, C:I.132 Water bridges: B:K.78, B:K.78, B:D.108, C:V.122, C:R.123, C:R.123 Salt bridges: B:K.110, B:K.110, C:R.121, C:R.121, C:R.123 pi-Stacking: B:F.112 ATP.12: 24 residues within 4Å: Chain A: G.47, M.48, T.49, E.82, L.83, V.84, R.121, R.123, I.132 Chain C: I.27, G.55, R.56, G.57, I.58, Q.59, K.78, Q.106, G.107, D.108, G.109, K.110, F.112 Ligands: AKG.7, MG.11 21 PLIP interactions: 9 interactions with chain A, 12 interactions with chain C Hydrogen bonds: A:T.49, A:V.84, A:V.84, A:I.132, C:G.57, C:I.58, C:Q.59, C:Q.59, C:G.107, C:G.109 Water bridges: A:V.122, A:R.123, C:K.78, C:K.78, C:D.108 Salt bridges: A:R.121, A:R.121, A:R.123, C:K.110, C:K.110 pi-Stacking: C:F.112

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

MES.8: 4 residues within 4Å: Chain C: R.29, E.31, R.32, T.103 3 PLIP interactions: 3 interactions with chain C Water bridges: C:R.29 Salt bridges: C:E.31, C:R.32

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 5 residues within 4Å: Chain C: Q.59, G.60, G.61, V.63, T.72 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.61, C:T.72 Water bridges: C:G.60

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.10: 6 residues within 4Å: Chain A: K.23, I.114 Chain B: K.23, I.114 Chain C: K.23, I.114 Ligand excluded by 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

GlnK2 from Methanothermococcus thermolithotrophicus: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

GlnK2 from Methanothermococcus thermolithotrophicus

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