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

Structure of AMPK in complex with Br2-A769662core activator and STAUROSPORINE inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.55 Å

Oligo State

hetero-2-2-2-mer

Ligands

2 x STU: STAUROSPORINE(Non-covalent)

STU.1: 21 residues within 4Å: Chain A: L.24, G.25, V.26, G.27, V.32, A.45, K.47, 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.3 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.24, A:A.45, A:Y.97, A:L.148, A:D.159 Hydrogen bonds: A:E.96, A:V.98, A:E.145 STU.11: 21 residues within 4Å: Chain D: L.24, G.25, V.26, G.27, V.32, A.45, K.47, 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.13 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:L.24, D:A.45, D:Y.97, D:L.148, D:D.159 Hydrogen bonds: D:E.96, D:V.98, D:E.145

2 x 32H: 2-bromo-3-(4-bromophenyl)-4-hydroxy-6-oxo-6,7-dihydrothieno[2,3-b]pyridine-5-carbonitrile(Non-covalent)

32H.2: 11 residues within 4Å: Chain A: K.31, K.33, I.48, K.53, D.90, F.92 Chain B: V.15, R.17, D.42, V.47, I.49 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:K.33, A:I.48, B:D.42, B:V.47 Hydrogen bonds: A:K.31, A:N.50, A:D.90 pi-Cation interactions: A:K.33, B:R.17 32H.12: 11 residues within 4Å: Chain D: K.31, K.33, I.48, K.53, D.90, F.92 Chain E: V.15, R.17, D.42, V.47, I.49 10 PLIP interactions: 6 interactions with chain D, 4 interactions with chain E Hydrophobic interactions: D:K.33, D:I.48, E:D.42, E:V.47 Hydrogen bonds: D:K.31, D:N.50, D:D.90, E:D.42 pi-Cation interactions: D:K.33, E:R.17

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

CL.3: 4 residues within 4Å: Chain A: G.25, V.26, G.27 Ligands: STU.1 Ligand excluded by PLIP CL.4: 1 residues within 4Å: Chain A: K.43 Ligand excluded by PLIP CL.5: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain A: S.99, D.150, A.151 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain B: T.19, D.70 Ligand excluded by PLIP CL.13: 4 residues within 4Å: Chain D: G.25, V.26, G.27 Ligands: STU.11 Ligand excluded by PLIP CL.14: 1 residues within 4Å: Chain D: K.43 Ligand excluded by PLIP CL.15: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain D: S.99, D.150, A.151 Ligand excluded by PLIP CL.17: 2 residues within 4Å: Chain E: T.19, D.70 Ligand excluded by PLIP

2 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.8: 12 residues within 4Å: Chain C: H.150, I.203, A.204, V.224, S.225, A.226, P.228, H.297, R.298, S.313, S.315, D.316 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:A.204, C:A.204, C:S.225, C:R.298, C:S.313, C:S.315, C:D.316 Salt bridges: C:H.150, C:H.297 AMP.18: 12 residues within 4Å: Chain F: H.150, I.203, A.204, V.224, S.225, A.226, P.228, H.297, R.298, S.313, S.315, D.316 9 PLIP interactions: 9 interactions with chain F Hydrogen bonds: F:A.204, F:A.204, F:S.225, F:R.298, F:S.313, F:S.315, F:D.316 Salt bridges: F:H.150, F:H.297

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

SO4.9: 7 residues within 4Å: Chain C: R.69, T.86, T.88, I.149, H.150, R.151, K.242 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:T.86, C:H.150, C:R.151 Salt bridges: C:R.69, C:H.150, C:K.242 SO4.10: 6 residues within 4Å: Chain C: R.69, S.225, S.241, F.243, H.297, R.298 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.69, C:S.241, C:S.241 Salt bridges: C:R.298 SO4.19: 7 residues within 4Å: Chain F: R.69, T.86, T.88, I.149, H.150, R.151, K.242 8 PLIP interactions: 8 interactions with chain F Hydrogen bonds: F:T.86, F:T.86, F:T.88, F:H.150, F:R.151 Salt bridges: F:R.69, F:H.150, F:K.242 SO4.20: 6 residues within 4Å: Chain F: R.69, S.225, S.241, F.243, H.297, R.298 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:R.69, F:S.241, F:S.241 Salt bridges: 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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