SMTL ID : 4zhx.1 (1 other biounit)

Novel binding site for allosteric activation of AMPK

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.99 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x 4O7: (5S,6R,7R,9R,13cR,14R,16aS)-6-methoxy-5-methyl-7-(methylamino)-6,7,8,9,14,15,16,16a-octahydro-5H,13cH-5,9-epoxy-4b,9a,1 5-triazadibenzo[b,h]cyclonona[1,2,3,4-jkl]cyclopenta[e]-as-indacen-14-ol(Non-covalent)

4O7.1: 19 residues within 4Å: Chain A: L.35, G.36, V.37, G.38, V.43, A.56, K.58, I.90, M.106, E.107, Y.108, V.109, G.112, E.113, E.156, N.157, L.159, A.169, D.170 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.35, A:A.56, A:K.58, A:Y.108, A:E.113, A:L.159, A:L.159, A:A.169, A:D.170 Hydrogen bonds: A:E.107, A:V.109, A:V.109, A:E.156

1 x C1V: 3-[4-(2-hydroxyphenyl)phenyl]-4-oxidanyl-6-oxidanylidene-7H-thieno[2,3-b]pyridine-5-carbonitrile(Non-covalent)

C1V.2: 13 residues within 4Å: Chain A: V.24, L.31, G.32, K.42, K.44, I.59, D.101 Chain B: V.81, R.83, T.106, R.107, S.108, V.113 11 PLIP interactions: 9 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:V.24, A:L.31, A:I.59, B:V.113 Hydrogen bonds: A:K.42, A:K.44, A:K.44, A:K.44, A:D.101 pi-Cation interactions: A:K.44, B:R.83

2 x C2Z: 5-(5-hydroxyl-isoxazol-3-yl)-furan-2-phosphonic acid(Non-covalent)

C2Z.3: 9 residues within 4Å: Chain C: H.156, R.157, S.231, H.303, R.304, S.319, L.320, S.321 Ligands: C2Z.4 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:H.156 Hydrogen bonds: C:H.156, C:S.231, C:S.231, C:R.304, C:R.304, C:S.319, C:S.321 Water bridges: C:R.157, C:H.174 Salt bridges: C:R.157, C:H.303 pi-Cation interactions: C:H.174 C2Z.4: 10 residues within 4Å: Chain C: R.75, T.92, T.94, H.156, R.157, S.231, S.247, K.248, F.249 Ligands: C2Z.3 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:F.249 Hydrogen bonds: C:T.92, C:T.94, C:T.94, C:T.94, C:H.156, C:H.156, C:R.157, C:S.247, C:F.249 Salt bridges: C:R.75, C:H.303 pi-Cation interactions: C:R.157, C:K.248

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Langendorf, C.G. et al., Structural basis of allosteric and synergistic activation of AMPK by furan-2-phosphonic derivative C2 binding. Nat Commun (2016)

Release Date

2016-03-09

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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