SMTL ID : 7lnx.1

I146A mutant of the isopentenyl phosphate kinase from Candidatus methanomethylophilus alvus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

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

ADP.1: 18 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, L.194, Y.195, T.196, A.197, D.198, P.199, K.200 Ligands: Y7D.2 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:G.28, A:S.29, A:S.29, A:V.188, A:S.189, A:D.190, A:Y.195, A:Y.195, A:K.200 Water bridges: A:K.25, A:K.25 Salt bridges: A:K.25, A:K.34, A:K.34 ADP.3: 17 residues within 4Å: Chain B: K.25, G.27, G.28, S.29, K.34, V.188, S.189, D.190, I.191, G.193, L.194, Y.195, A.197, D.198, P.199, K.200, K.235 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:G.28, B:S.29, B:S.29, B:S.189, B:D.190, B:Y.195, B:Y.195 Water bridges: B:K.25, B:K.25, B:K.25, B:K.34, B:K.34 Salt bridges: B:K.25, B:K.34, B:K.34 pi-Cation interactions: B:K.235

1 x Y7D: (2Z)-3-methylhept-2-en-1-yl trihydrogen diphosphate(Non-covalent)

Y7D.2: 17 residues within 4Å: Chain A: K.25, G.28, K.34, G.64, A.65, G.66, G.69, H.70, A.73, Q.79, G.154, D.155, A.166, V.167, S.168, G.169 Ligands: ADP.1 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:A.65, A:A.73, A:Q.79, A:A.166 Hydrogen bonds: A:G.28, A:A.65, A:G.66, A:G.169 Water bridges: A:K.25, A:K.25 Salt bridges: A:K.25, A:K.25, A:K.34, A:H.70, A:H.70

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain B: R.17, G.18, M.21, D.58, A.144, D.145, F.180 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.58, B:A.144

1 x WOG: (2E)-3-methylhept-2-en-1-yl dihydrogen phosphate(Non-covalent)

WOG.5: 14 residues within 4Å: Chain B: K.25, G.64, A.65, G.66, G.69, H.70, A.73, G.154, D.155, V.156, A.166, V.167, S.168, G.169 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:A.65, B:A.73, B:V.156, B:A.166 Hydrogen bonds: B:A.65, B:G.66, B:G.169 Water bridges: B:K.25, B:K.25, B:K.25, B:K.25, B:G.28, B:G.28 Salt bridges: B:K.25, B: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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