SMTL ID : 6c9f.1

AMP-activated protein kinase bound to pharmacological activator R734

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.92 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x R34: 5-{[6-chloro-5-(1-methyl-1H-indol-5-yl)-1H-benzimidazol-2-yl]oxy}-N-hydroxy-2-methylbenzamide(Non-covalent)

R34.1: 16 residues within 4Å: Chain A: V.11, L.18, T.26, F.27, G.28, K.29, K.31, I.46, N.48, K.51, D.88, F.90 Chain B: V.15, R.17, D.42, V.47 16 PLIP interactions: 11 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:V.11, A:L.18, A:K.31, A:I.46, A:K.51, B:D.42, B:V.47, B:V.47 Hydrogen bonds: A:G.28, A:G.28, A:N.48, A:D.88, B:R.17 pi-Cation interactions: A:K.31, A:K.31, B:R.17

1 x STU: STAUROSPORINE(Non-covalent)

STU.2: 17 residues within 4Å: Chain A: L.22, G.23, V.24, V.30, A.43, K.45, M.93, E.94, Y.95, V.96, G.99, E.100, E.143, N.144, L.146, A.156, D.157 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.22, A:V.30, A:K.45, A:E.100, A:L.146, A:D.157 Hydrogen bonds: A:V.96, A:E.143

3 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.3: 11 residues within 4Å: Chain C: M.85, T.87, T.89, D.90, P.128, L.129, V.130, I.150, H.151, R.152, P.154 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:T.87, C:D.90, C:V.130, C:H.151, C:R.152 Salt bridges: C:H.151, C:K.243 AMP.4: 12 residues within 4Å: Chain C: R.70, I.240, S.242, F.244, D.245, R.269, G.275, V.276, L.277, V.297, H.298, R.299 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:S.242, C:D.245, C:R.269, C:R.269, C:L.277, C:L.277, C:H.298, C:R.299 Salt bridges: C:R.70, C:K.170, C:H.298, C:R.299 AMP.5: 14 residues within 4Å: Chain C: H.151, T.200, N.203, I.204, A.205, V.225, S.226, A.227, P.229, R.299, I.312, S.314, S.316, D.317 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:T.200, C:T.200, C:A.205, C:A.205, C:S.226, C:S.226, C:S.226, C:S.226, C:S.314, C:S.316, C:D.317 Salt bridges: C:H.151

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yan, Y. et al., Structures of AMP-activated protein kinase bound to novel pharmacological activators in phosphorylated, non-phosphorylated, and nucleotide-free states. J. Biol. Chem. (2019)

Release Date

2018-11-28

Peptides

5'-AMP-activated protein kinase catalytic subunit alpha-1,5'-AMP-activated protein kinase catalytic subunit alpha-1: A
5'-AMP-activated protein kinase subunit beta-1: B
5'-AMP-activated protein kinase subunit gamma-1: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

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