SMTL ID : 3lcb.3 (2 other biounits)

The crystal structure of isocitrate dehydrogenase kinase/phosphatase in complex with its substrate, isocitrate dehydrogenase, from Escherichia coli.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

hetero-6-6-mer

Ligands

6 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.1: 14 residues within 4Å: Chain A: 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 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:N.104, A:T.295, A:E.376 Salt bridges: A:H.113, A:K.291, A:K.294 pi-Stacking: A:Y.298, A:F.375, A:F.375 AMP.5: 13 residues within 4Å: Chain B: N.104, S.105, C.108, H.113, L.116, K.291, K.294, T.295, Y.298, F.375, E.376, N.377, F.378 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:N.104, B:H.113, B:T.295, B:T.295, B:N.377 Salt bridges: B:H.113, B:K.291, B:K.294 pi-Stacking: B:Y.298, B:F.375, B:F.375 AMP.7: 14 residues within 4Å: Chain E: 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 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:N.104, E:T.295, E:E.376 Salt bridges: E:H.113, E:K.291, E:K.294 pi-Stacking: E:Y.298, E:F.375, E:F.375 AMP.11: 13 residues within 4Å: Chain F: N.104, S.105, C.108, H.113, L.116, K.291, K.294, T.295, Y.298, F.375, E.376, N.377, F.378 11 PLIP interactions: 11 interactions with chain F Hydrogen bonds: F:N.104, F:H.113, F:T.295, F:T.295, F:N.377 Salt bridges: F:H.113, F:K.291, F:K.294 pi-Stacking: F:Y.298, F:F.375, F:F.375 AMP.13: 14 residues within 4Å: Chain I: 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 9 PLIP interactions: 9 interactions with chain I Hydrogen bonds: I:N.104, I:T.295, I:E.376 Salt bridges: I:H.113, I:K.291, I:K.294 pi-Stacking: I:Y.298, I:F.375, I:F.375 AMP.17: 13 residues within 4Å: Chain J: N.104, S.105, C.108, H.113, L.116, K.291, K.294, T.295, Y.298, F.375, E.376, N.377, F.378 11 PLIP interactions: 11 interactions with chain J Hydrogen bonds: J:N.104, J:H.113, J:T.295, J:T.295, J:N.377 Salt bridges: J:H.113, J:K.291, J:K.294 pi-Stacking: J:Y.298, J:F.375, J:F.375

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

ATP.2: 24 residues within 4Å: Chain A: P.316, G.317, I.318, R.319, G.320, M.321, V.322, M.323, V.325, V.334, K.336, K.346, E.416, R.417, R.418, M.419, P.421, D.457, K.461, N.462, Y.474, D.475, D.477 Ligands: MG.3 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:I.318, A:M.321, A:V.322, A:M.323, A:E.416, A:M.419, A:D.457, A:N.462, A:D.475, A:D.475 Salt bridges: A:K.336, A:K.346, A:K.461 pi-Stacking: A:Y.474 ATP.4: 22 residues within 4Å: Chain B: P.316, I.318, G.320, M.321, V.322, M.323, V.325, V.334, K.336, K.346, E.416, R.417, R.418, M.419, P.421, D.457, K.461, N.462, Y.474, D.475, D.477 Ligands: MG.6 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:M.321, B:V.322, B:M.323, B:E.416, B:E.416, B:M.419, B:D.457, B:D.477 Salt bridges: B:K.346, B:K.346, B:K.461, B:K.461 pi-Stacking: B:Y.474 ATP.8: 24 residues within 4Å: Chain E: P.316, G.317, I.318, R.319, G.320, M.321, V.322, M.323, V.325, V.334, K.336, K.346, E.416, R.417, R.418, M.419, P.421, D.457, K.461, N.462, Y.474, D.475, D.477 Ligands: MG.9 13 PLIP interactions: 13 interactions with chain E Hydrogen bonds: E:M.321, E:V.322, E:M.323, E:E.416, E:M.419, E:D.457, E:N.462, E:D.475, E:D.475 Salt bridges: E:K.336, E:K.346, E:K.461 pi-Stacking: E:Y.474 ATP.10: 22 residues within 4Å: Chain F: P.316, I.318, G.320, M.321, V.322, M.323, V.325, V.334, K.336, K.346, E.416, R.417, R.418, M.419, P.421, D.457, K.461, N.462, Y.474, D.475, D.477 Ligands: MG.12 13 PLIP interactions: 13 interactions with chain F Hydrogen bonds: F:M.321, F:V.322, F:M.323, F:E.416, F:E.416, F:M.419, F:D.457, F:D.477 Salt bridges: F:K.346, F:K.346, F:K.461, F:K.461 pi-Stacking: F:Y.474 ATP.14: 24 residues within 4Å: Chain I: P.316, G.317, I.318, R.319, G.320, M.321, V.322, M.323, V.325, V.334, K.336, K.346, E.416, R.417, R.418, M.419, P.421, D.457, K.461, N.462, Y.474, D.475, D.477 Ligands: MG.15 14 PLIP interactions: 14 interactions with chain I Hydrogen bonds: I:I.318, I:M.321, I:V.322, I:M.323, I:E.416, I:M.419, I:D.457, I:N.462, I:D.475, I:D.475 Salt bridges: I:K.336, I:K.346, I:K.461 pi-Stacking: I:Y.474 ATP.16: 22 residues within 4Å: Chain J: P.316, I.318, G.320, M.321, V.322, M.323, V.325, V.334, K.336, K.346, E.416, R.417, R.418, M.419, P.421, D.457, K.461, N.462, Y.474, D.475, D.477 Ligands: MG.18 13 PLIP interactions: 13 interactions with chain J Hydrogen bonds: J:M.321, J:V.322, J:M.323, J:E.416, J:E.416, J:M.419, J:D.457, J:D.477 Salt bridges: J:K.346, J:K.346, J:K.461, J:K.461 pi-Stacking: J:Y.474

6 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: N.462, D.475 Ligands: ATP.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.475, A:D.475 MG.6: 3 residues within 4Å: Chain B: N.462, D.475 Ligands: ATP.4 No protein-ligand interaction detected (PLIP) MG.9: 3 residues within 4Å: Chain E: N.462, D.475 Ligands: ATP.8 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.475, E:D.475 MG.12: 3 residues within 4Å: Chain F: N.462, D.475 Ligands: ATP.10 No protein-ligand interaction detected (PLIP) MG.15: 3 residues within 4Å: Chain I: N.462, D.475 Ligands: ATP.14 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:D.475, I:D.475 MG.18: 3 residues within 4Å: Chain J: N.462, D.475 Ligands: ATP.16 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zheng, J. et al., Structure of the bifunctional isocitrate dehydrogenase kinase/phosphatase. Nature (2010)

Release Date

2010-04-21

Peptides

Isocitrate dehydrogenase kinase/phosphatase: ABEFIJ
Isocitrate dehydrogenase [NADP]: CDGHKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

E
A

F
B

I
A

J
B

C
C

D
D

G
C

H
D

K
C

L
D

Isocitrate dehydrogenase kinase/phosphatase

Isocitrate dehydrogenase [NADP]

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