SMTL ID : 7lnt.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-dimer

Ligands

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 10 residues within 4Å: Chain A: R.99, S.118, V.119, A.120, S.123 Chain B: S.118, V.119, A.120, S.123, C.124 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.118, A:A.120, A:S.123, B:A.120 Water bridges: A:A.120, B:S.123 GOL.4: 6 residues within 4Å: Chain A: C.124, N.136 Chain B: C.124, F.125, D.135, N.136 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:D.135, B:N.136, A:C.124, A:N.136, A:N.136 Water bridges: B:N.136

2 x WZT: (phenylmethyl) dihydrogen phosphate(Non-covalent)

WZT.2: 13 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 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:A.65, A:A.73, A:I.94, A:I.166 Hydrogen bonds: A:A.65, A:G.66, A:G.169 Water bridges: A:K.25, A:G.28, A:K.34, A:H.70, A:D.170 Salt bridges: A:K.25, A:H.70 WZT.5: 13 residues within 4Å: Chain B: 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 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:A.65, B:A.73, B:I.94, B:I.166 Hydrogen bonds: B:A.65, B:G.66, B:G.169 Water bridges: B:K.25, B:K.25, B:D.170 Salt bridges: B:H.70 pi-Stacking: B:H.70

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

ADP.3: 16 residues within 4Å: Chain A: K.25, G.27, G.28, S.29, K.34, V.188, S.189, D.190, I.191, G.193, Y.195, A.197, D.198, P.199, K.200, K.235 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:G.28, A:S.29, A:S.29, A:V.188, A:D.190, A:Y.195, A:Y.195 Water bridges: A:K.25, A:K.25, A:G.27, A:G.27, A:K.34 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, P.199, V.232, K.235 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:G.27, B:G.28, B:S.29, B:D.190, B:Y.195, B:Y.195, B:K.235 Water bridges: B:K.25, B:K.25, B:K.25 Salt bridges: B:K.25, B:K.34 pi-Cation interactions: B:K.235

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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