SMTL ID : 4qfg.2 (1 other biounit)

Structure of AMPK in complex with STAUROSPORINE inhibitor and in the absence of a synthetic activator

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.46 Å

Oligo State

hetero-2-2-2-mer

Ligands

2 x STU: STAUROSPORINE(Non-covalent)

STU.1: 22 residues within 4Å: Chain A: L.24, G.25, V.26, G.27, V.32, A.45, K.47, E.66, I.79, M.95, E.96, Y.97, V.98, S.99, G.101, E.102, E.145, N.146, L.148, A.158, D.159 Ligands: CL.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.24, A:L.24, A:L.24, A:V.32, A:A.45, A:Y.97, A:E.102, A:L.148 Hydrogen bonds: A:E.96, A:V.98, A:E.145 STU.9: 22 residues within 4Å: Chain D: L.24, G.25, V.26, G.27, V.32, A.45, K.47, E.66, I.79, M.95, E.96, Y.97, V.98, S.99, G.101, E.102, E.145, N.146, L.148, A.158, D.159 Ligands: CL.10 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:L.24, D:L.24, D:L.24, D:V.32, D:A.45, D:Y.97, D:E.102, D:L.148 Hydrogen bonds: D:E.96, D:V.98, D:E.102, D:E.145

6 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 2 residues within 4Å: Chain A: V.26 Ligands: STU.1 Ligand excluded by PLIP CL.3: 2 residues within 4Å: Chain A: K.36, K.43 Ligand excluded by PLIP CL.4: 2 residues within 4Å: Chain A: S.99, A.151 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain D: V.26 Ligands: STU.9 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain D: K.36, K.43 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain D: S.99, A.151 Ligand excluded by PLIP

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 6 residues within 4Å: Chain A: K.31, N.50, K.53 Chain B: R.17, N.44, N.45 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Salt bridges: A:K.31, A:K.53, B:R.17 Hydrogen bonds: B:N.45 SO4.7: 6 residues within 4Å: Chain C: T.86, I.87, T.88, H.150, R.151, K.242 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:T.86, C:I.87, C:T.88, C:T.88, C:T.88 Salt bridges: C:H.150, C:R.151, C:K.242 SO4.8: 5 residues within 4Å: Chain C: S.241, K.242, F.243, H.297, R.298 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:S.241, C:K.242, C:F.243 Salt bridges: C:H.297, C:R.298 SO4.13: 6 residues within 4Å: Chain D: K.31, N.50, K.53 Chain E: R.17, N.44, N.45 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain D Hydrogen bonds: E:N.45 Salt bridges: E:R.17, D:K.31, D:K.53 SO4.15: 6 residues within 4Å: Chain F: T.86, I.87, T.88, H.150, R.151, K.242 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:I.87, F:T.88, F:T.88, F:T.88 Salt bridges: F:H.150, F:R.151, F:K.242 SO4.16: 5 residues within 4Å: Chain F: S.241, K.242, F.243, H.297, R.298 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:S.241, F:K.242, F:F.243 Salt bridges: F:H.297, F:R.298

2 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.6: 13 residues within 4Å: Chain C: H.150, T.199, N.202, I.203, A.204, V.224, S.225, A.226, R.298, I.311, S.313, S.315, D.316 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:T.199, C:A.204, C:A.204, C:S.225, C:S.313, C:S.315, C:D.316 Salt bridges: C:H.150, C:R.298 AMP.14: 13 residues within 4Å: Chain F: H.150, T.199, N.202, I.203, A.204, V.224, S.225, A.226, R.298, I.311, S.313, S.315, D.316 10 PLIP interactions: 10 interactions with chain F Hydrogen bonds: F:T.199, F:T.199, F:A.204, F:A.204, F:S.225, F:S.313, F:S.315, F:D.316 Salt bridges: F:H.150, F:R.298

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Calabrese, M.F. et al., Structural Basis for AMPK Activation: Natural and Synthetic Ligands Regulate Kinase Activity from Opposite Poles by Different Molecular Mechanisms. Structure (2014)

Release Date

2014-08-06

Peptides

5'-AMP-activated protein kinase catalytic subunit alpha-1: AD
5'-AMP-activated protein kinase subunit beta-1: BE
5'-AMP-activated protein kinase subunit gamma-1: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
A

B
B

E
B

C
C

F
C

5'-AMP-activated protein kinase catalytic subunit alpha-1

5'-AMP-activated protein kinase subunit beta-1

5'-AMP-activated protein kinase subunit gamma-1

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