SMTL ID : 6k5l.1

The crystal structure of isocitrate dehydrogenase kinase/phosphatase wtih two Mn2+ from E. coli

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

homo-dimer

Ligands

2 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.1: 17 residues within 4Å: Chain A: Y.54, S.101, N.104, S.105, C.108, H.113, L.116, L.121, K.291, K.294, T.295, Y.298, F.375, E.376, N.377, F.378, V.379 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:N.104, A:S.105, A:E.376 Water bridges: A:R.109, A:K.291, A:E.376, A:V.379 Salt bridges: A:H.113, A:K.291, A:K.294 pi-Stacking: A:F.375, A:F.375 AMP.5: 17 residues within 4Å: Chain B: Y.54, S.101, N.104, S.105, C.108, H.113, L.116, L.121, K.291, K.294, T.295, Y.298, F.375, E.376, N.377, F.378, V.379 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:N.104, B:S.105, B:E.376 Water bridges: B:K.291, B:K.294, B:E.376 Salt bridges: B:H.113, B:K.291, B:K.294 pi-Stacking: B:Y.298, B:F.375, B:F.375

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

ADP.2: 24 residues within 4Å: Chain A: A.315, P.316, G.317, I.318, R.319, G.320, M.321, V.322, M.323, V.325, V.334, K.336, E.416, R.417, R.418, M.419, P.421, K.461, N.462, Y.474, D.475, D.477 Ligands: MN.3, MN.4 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:I.318, A:I.318, A:I.318, A:M.321, A:V.322, A:M.323, A:K.336, A:E.416, A:M.419, A:N.462 Water bridges: A:Y.476 Salt bridges: A:K.336 pi-Stacking: A:Y.474 ADP.6: 26 residues within 4Å: Chain B: A.315, P.316, G.317, I.318, R.319, G.320, M.321, V.322, M.323, V.325, V.334, K.336, K.346, Y.357, E.416, R.417, R.418, M.419, P.421, K.461, N.462, Y.474, D.475, D.477 Ligands: MN.7, MN.8 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:I.318, B:I.318, B:I.318, B:M.321, B:V.322, B:M.323, B:K.336, B:E.416, B:E.416, B:M.419, B:Y.474 Water bridges: B:K.461 Salt bridges: B:K.336, B:K.346 pi-Stacking: B:Y.474

4 x MN: MANGANESE (II) ION(Non-covalent)

MN.3: 3 residues within 4Å: Chain A: N.462, D.475 Ligands: ADP.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.475 MN.4: 5 residues within 4Å: Chain A: V.322, K.346, D.475, D.477 Ligands: ADP.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.475, A:D.475, A:D.477, A:D.477, H2O.2 MN.7: 3 residues within 4Å: Chain B: N.462, D.475 Ligands: ADP.6 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.475 MN.8: 5 residues within 4Å: Chain B: V.322, K.346, D.475, D.477 Ligands: ADP.6 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.475, B:D.475, B:D.477

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, X. et al., Characterization of metal binding of bifunctional kinase/phosphatase AceK and implication in activity modulation. Sci Rep (2019)

Release Date

2019-07-03

Peptides

Isocitrate dehydrogenase kinase/phosphatase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Isocitrate dehydrogenase kinase/phosphatase

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