SMTL ID : 7lnu.1

Ternary complex of the Isopentenyl Phosphate Kinase from Candidatus methanomethylophilus alvus bound to isopentenyl monophosphate and ATP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

2 x IP8: Isopentenyl phosphate(Non-covalent)

IP8.1: 15 residues within 4Å: Chain A: G.64, A.65, G.66, G.69, H.70, A.73, I.94, G.154, D.155, I.166, V.167, S.168, G.169 Ligands: ATP.3, IPE.4 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:A.73, A:I.94, A:I.166 Hydrogen bonds: A:A.65, A:G.66, A:G.169 Water bridges: A:D.170 Salt bridges: A:K.34, A:H.70 IP8.5: 11 residues within 4Å: Chain B: G.64, A.65, G.66, G.69, H.70, G.154, D.155, I.166, V.167, S.168, G.169 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:A.65, B:I.166 Hydrogen bonds: B:A.65, B:G.66, B:G.169 Water bridges: B:G.28, B:S.168 Salt bridges: B:H.70

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

ADP.2: 16 residues within 4Å: Chain A: K.25, G.27, G.28, S.29, K.34, S.189, D.190, I.191, L.194, Y.195, A.197, D.198, K.200, K.235 Ligands: ATP.3, IPE.4 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:G.28, A:S.29, A:S.29, A:S.189, A:Y.195, A:K.200, A:K.235 Water bridges: A:K.25, A:K.25, A:K.25, A:K.25 Salt bridges: A:K.25, A:K.34, A:K.34 pi-Cation interactions: A:K.235 ADP.6: 15 residues within 4Å: Chain B: K.25, G.27, G.28, S.29, S.189, D.190, I.191, G.193, L.194, Y.195, A.197, D.198, K.200, V.232, K.235 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:G.28, B:S.29, B:S.29, B:S.29, B:D.190, B:Y.195, B:Y.195, B:K.235 Water bridges: B:K.25 Salt bridges: B:K.25 pi-Cation interactions: B:K.235

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

ATP.3: 20 residues within 4Å: Chain A: K.25, G.27, G.28, S.29, K.34, G.64, H.70, V.188, S.189, D.190, I.191, L.194, Y.195, A.197, D.198, K.200, K.235 Ligands: IP8.1, ADP.2, IPE.4 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:G.28, A:S.29, A:S.29, A:H.70, A:S.189, A:Y.195, A:Y.195, A:K.200, A:K.235 Water bridges: A:K.25, A:K.25, A:K.25, A:K.25, A:K.25, A:D.170 Salt bridges: A:K.25, A:K.25, A:K.34, A:K.34 pi-Cation interactions: A:K.235

1 x IPE: 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE(Non-covalent)

IPE.4: 16 residues within 4Å: Chain A: K.34, G.64, A.65, G.66, G.69, H.70, G.154, D.155, I.166, V.167, S.168, G.169, D.170 Ligands: IP8.1, ADP.2, ATP.3 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:A.65, A:I.166 Hydrogen bonds: A:A.65, A:G.66, A:G.169 Salt bridges: A:K.34, A:K.34, A:H.70, A:H.70

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Johnson, B.P. et al., Molecular Basis for the Substrate Promiscuity of Isopentenyl Phosphate Kinase from Candidatus methanomethylophilus alvus . Acs Chem.Biol. (2022)

Release Date

2021-12-22

Peptides

Isopentenyl phosphate kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Isopentenyl phosphate kinase

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