SMTL ID : 4zhx.2 (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: 18 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, E.113, E.156, N.157, L.159, A.169, D.170 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.35, A:V.43, A:A.56, A:K.58, A:Y.108, 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: 15 residues within 4Å: Chain A: V.24, L.31, G.32, K.42, K.44, I.59, N.61, D.101, F.103 Chain B: V.81, R.83, T.106, R.107, S.108, V.113 15 PLIP interactions: 4 interactions with chain B, 11 interactions with chain A Hydrophobic interactions: B:T.106, B:V.113, A:V.24, A:V.24, A:L.31, A:K.44, A:I.59 Hydrogen bonds: B:N.111, A:K.42, A:K.44, A:K.44, A:K.44, A:D.101 pi-Cation interactions: B:R.83, A:K.44

2 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.3: 14 residues within 4Å: Chain A: P.380 Chain C: R.75, K.175, I.245, S.247, F.249, D.250, R.274, F.278, V.281, L.282, V.302, H.303, R.304 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:S.247, C:D.250, C:L.282, C:L.282, C:H.303, C:R.304 Water bridges: C:K.248, C:D.250 Salt bridges: C:R.75, C:K.175, C:R.304 AMP.4: 14 residues within 4Å: Chain C: H.156, T.205, N.208, I.209, A.210, V.230, S.231, A.232, H.303, R.304, I.317, S.319, S.321, D.322 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:T.205, C:A.210, C:A.210, C:S.231, C:S.231, C:R.304, C:S.319, C:S.321, C:D.322 Salt bridges: C:H.156, C:H.303

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
C

B
D

C
F

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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