SMTL ID : 6c8z.1

Last common ancestor of ADP-dependent phosphofructokinases from Methanosarcinales

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.86 Å

Oligo State

homo-dimer

Ligands

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 15 residues within 4Å: Chain A: D.331, H.381, S.382, L.383, A.416, K.479, V.480, V.481, P.484, G.489, I.490, G.491, D.492, I.494 Ligands: MG.5 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:D.331, A:D.331, A:S.382, A:V.481, A:V.481, A:G.489, A:I.490, A:G.491, A:D.492 Water bridges: A:D.331 Salt bridges: A:H.381 ADP.6: 15 residues within 4Å: Chain B: D.331, H.381, S.382, L.383, A.416, K.479, V.480, V.481, P.484, G.489, I.490, G.491, D.492, I.494 Ligands: MG.10 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:D.331, B:H.381, B:S.382, B:V.481, B:V.481, B:G.489, B:I.490, B:G.491, B:D.492 Water bridges: B:E.303, B:E.303, B:D.331, B:D.492 Salt bridges: B:H.381

6 x NI: NICKEL (II) ION(Non-covalent)

NI.2: 5 residues within 4Å: Chain A: H.248, E.251 Chain B: L.184, H.248 Ligands: NI.7 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Metal complexes: A:H.248, A:E.251, B:H.248 NI.3: 1 residues within 4Å: Chain A: D.319 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.319, A:D.319 NI.4: 3 residues within 4Å: Chain A: D.63, D.65, D.66 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.63, A:D.63, A:D.65, A:D.66 NI.7: 5 residues within 4Å: Chain A: L.184, H.248 Chain B: H.248, E.251 Ligands: NI.2 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Metal complexes: B:H.248, B:E.251, A:H.248 NI.8: 1 residues within 4Å: Chain B: D.319 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.319, B:D.319 NI.9: 3 residues within 4Å: Chain B: D.63, D.65, D.66 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.63, B:D.63, B:D.65, B:D.66

2 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 3 residues within 4Å: Chain A: E.334, D.492 Ligands: ADP.1 No protein-ligand interaction detected (PLIP) MG.10: 3 residues within 4Å: Chain B: E.334, D.492 Ligands: ADP.6 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gonzalez-Ordenes, F. et al., ADP-Dependent Kinases From the Archaeal OrderMethanosarcinalesAdapt to Salt by a Non-canonical Evolutionarily Conserved Strategy. Front Microbiol (2018)

Release Date

2018-02-07

Peptides

ADP-dependent phosphofructokinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

ADP-dependent phosphofructokinase

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