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

Structure of full length human AMPK in complex with a small molecule activator, a benzimidazole derivative (991)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.02 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x STU: STAUROSPORINE(Non-covalent)

STU.1: 17 residues within 4Å: Chain A: L.41, G.42, V.43, G.44, V.49, A.62, K.64, I.96, M.112, E.113, Y.114, V.115, E.119, E.162, N.163, L.165, D.176 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.41, A:V.49, A:V.49, A:K.64, A:Y.114, A:L.165, A:D.176 Hydrogen bonds: A:V.115, A:E.162

1 x 992: 5-[[6-chloranyl-5-(1-methylindol-5-yl)-1H-benzimidazol-2-yl]oxy]-2-methyl-benzoic acid(Non-covalent)

992.2: 17 residues within 4Å: Chain A: V.30, L.37, V.43, G.47, K.48, K.50, I.65, N.67, D.107, F.109 Chain B: V.97, R.99, T.122, R.123, S.124, N.127, V.129 15 PLIP interactions: 3 interactions with chain B, 12 interactions with chain A Hydrophobic interactions: B:N.127, B:V.129, A:V.30, A:L.37, A:V.43, A:K.48, A:K.50, A:I.65, A:I.65 pi-Cation interactions: B:R.99, A:K.50, A:K.50 Hydrogen bonds: A:K.48, A:D.107 Salt bridges: A:K.48

3 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.3: 12 residues within 4Å: Chain C: M.85, T.87, T.89, D.90, Y.121, P.128, L.129, V.130, I.150, H.151, R.152, P.154 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:T.87, C:T.89, C:D.90, C:Y.121, C:Y.121, C:V.130, C:V.130, C:H.151, C:R.152, C:R.152 Salt bridges: C:H.151 AMP.4: 14 residues within 4Å: Chain A: P.386, E.387 Chain C: R.70, K.170, I.240, S.242, F.244, D.245, R.269, V.276, L.277, V.297, H.298, R.299 12 PLIP interactions: 11 interactions with chain C, 1 interactions with chain A 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, A:P.386 Salt bridges: C:R.70, C:K.170, 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, H.298, 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.314, C:S.316, C:D.317 Salt bridges: C:H.151, C:H.298

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xiao, B. et al., Structural Basis of Ampk Regulation by Small Molecule Activators. Nat.Commun. (2013)

Release Date

2013-12-25

Peptides

5'-AMP-ACTIVATED PROTEIN KINASE CATALYTIC SUBUNIT ALPHA-2: 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
E

5'-AMP-ACTIVATED PROTEIN KINASE CATALYTIC SUBUNIT ALPHA-2

5'-AMP-ACTIVATED PROTEIN KINASE SUBUNIT BETA-1

5'-AMP-ACTIVATED PROTEIN KINASE SUBUNIT GAMMA-1

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