SMTL ID : 7p4v.1

GlnK1 from Methanothermococcus thermolithotrophicus with dADP at a resolution of 1.94 A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.94 Å

Oligo State

homo-trimer

Ligands

3 x DAT: 2'-DEOXYADENOSINE-5'-DIPHOSPHATE(Non-covalent)

DAT.1: 21 residues within 4Å: Chain A: G.55, R.56, G.57, I.58, Q.59, K.78, F.106, G.107, D.108, G.109, K.110, F.112 Chain C: G.47, M.48, T.49, E.82, M.83, A.84, R.121, R.123, I.132 18 PLIP interactions: 12 interactions with chain A, 6 interactions with chain C Hydrogen bonds: A:I.58, A:Q.59, A:G.107, A:D.108, A:G.109, A:G.109, C:T.49, C:A.84, C:A.84 Water bridges: A:K.78, A:K.78, A:K.110, A:K.110, C:G.47 Salt bridges: A:K.110, A:K.110, C:R.121, C:R.123 DAT.4: 21 residues within 4Å: Chain A: G.47, M.48, T.49, E.82, M.83, A.84, R.121, R.123, I.132 Chain B: G.55, R.56, G.57, I.58, Q.59, K.78, F.106, G.107, D.108, G.109, K.110, F.112 18 PLIP interactions: 6 interactions with chain A, 12 interactions with chain B Hydrogen bonds: A:T.49, A:A.84, A:A.84, B:I.58, B:Q.59, B:G.107, B:D.108, B:G.109, B:G.109 Water bridges: A:G.47, B:K.78, B:K.78, B:K.110, B:K.110 Salt bridges: A:R.121, A:R.123, B:K.110, B:K.110 DAT.7: 21 residues within 4Å: Chain B: G.47, M.48, T.49, E.82, M.83, A.84, R.121, R.123, I.132 Chain C: G.55, R.56, G.57, I.58, Q.59, K.78, F.106, G.107, D.108, G.109, K.110, F.112 18 PLIP interactions: 12 interactions with chain C, 6 interactions with chain B Hydrogen bonds: C:I.58, C:Q.59, C:G.107, C:D.108, C:G.109, C:G.109, B:T.49, B:A.84, B:A.84 Water bridges: C:K.78, C:K.78, C:K.110, C:K.110, B:G.47 Salt bridges: C:K.110, C:K.110, B:R.121, B:R.123

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

CL.2: 6 residues within 4Å: Chain A: E.52 Chain B: E.52 Chain C: S.51, E.52 Ligands: CL.5, CL.8 Ligand excluded by PLIP CL.3: 5 residues within 4Å: Chain A: K.23 Chain B: K.23 Chain C: K.23 Ligands: CL.6, CL.9 Ligand excluded by PLIP CL.5: 6 residues within 4Å: Chain A: S.51, E.52 Chain B: E.52 Chain C: E.52 Ligands: CL.2, CL.8 Ligand excluded by PLIP CL.6: 5 residues within 4Å: Chain A: K.23 Chain B: K.23 Chain C: K.23 Ligands: CL.3, CL.9 Ligand excluded by PLIP CL.8: 6 residues within 4Å: Chain A: E.52 Chain B: S.51, E.52 Chain C: E.52 Ligands: CL.2, CL.5 Ligand excluded by PLIP CL.9: 5 residues within 4Å: Chain A: K.23 Chain B: K.23 Chain C: K.23 Ligands: CL.3, CL.6 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

GlnK1 from Methanothermococcus thermolithotrophicus: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

GlnK1 from Methanothermococcus thermolithotrophicus