SMTL ID : 7n9d.1

I74A mutant of the isopentenyl phosphate kinase from Candidatus methanomethylophilus alvus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

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

ADP.1: 18 residues within 4Å: Chain A: G.27, G.28, S.29, K.34, S.189, D.190, I.191, G.193, L.194, Y.195, A.197, D.198, L.220, T.221, D.222, G.231, V.232, K.235 28 PLIP interactions: 28 interactions with chain A Hydrogen bonds: A:S.29, A:S.29, A:S.189, A:D.190, A:Y.195, A:Y.195, A:D.222 Water bridges: A:K.25, A:K.25, A:G.28, A:G.28, A:G.28, A:K.34, A:K.34, A:K.34, A:V.188, A:S.189, A:D.190, A:D.198, A:G.231, A:G.231, A:V.232, A:V.232, A:K.235 Salt bridges: A:K.34, A:K.34, A:K.235, A:K.235 ADP.3: 20 residues within 4Å: Chain B: K.25, G.27, G.28, S.29, K.34, S.189, D.190, I.191, G.193, L.194, Y.195, A.197, D.198, P.199, K.200, L.220, T.221, G.231, V.232, K.235 21 PLIP interactions: 21 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, B:K.200 Water bridges: B:K.25, B:K.25, B:K.25, B:V.188, B:G.231, B:V.232, B:K.235, B:K.235 Salt bridges: B:K.25, B:K.34, B:K.34, B:K.235, B:K.235

2 x 0XI: (2E)-3-phenylbut-2-en-1-yl dihydrogen phosphate(Non-covalent)

0XI.2: 18 residues within 4Å: Chain A: K.25, G.64, A.65, G.66, G.69, H.70, A.73, A.94, M.95, T.98, G.154, D.155, V.156, I.166, V.167, S.168, G.169, T.229 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:A.65, A:A.73, A:A.94, A:V.156, A:I.166, A:I.166 Hydrogen bonds: A:A.65, A:G.66, A:G.154, A:G.169, A:T.229, A:T.229 Water bridges: A:K.25, A:K.25, A:S.168 Salt bridges: A:K.25, A:H.70 0XI.4: 16 residues within 4Å: Chain B: K.25, G.64, A.65, G.69, H.70, A.73, A.94, T.98, G.154, D.155, V.156, I.166, V.167, S.168, G.169, T.229 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:A.65, B:A.73, B:A.94, B:T.98, B:V.156, B:I.166, B:I.166 Hydrogen bonds: B:A.65, B:G.169 Water bridges: B:K.25, B:K.25, B:T.229, B:T.229 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