SMTL ID : 7jhh.1

Cryo-EM structure of ATP-bound fully inactive AMPK in complex with Fab and nanobody

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-mer

Ligands

1 x GLC- GLC: alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose(Non-covalent)

GLC-GLC.1: 13 residues within 4Å: Chain D: N.14, K.17, W.64, A.65, D.67, R.68, E.113, E.155, P.156, Y.157, W.232, W.342, R.346 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:D.67, D:R.68, D:Y.157, D:R.346

1 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.2: 17 residues within 4Å: Chain C: R.49, R.131, T.147, K.149, I.219, S.221, F.223, D.224, R.248, G.254, V.255, L.256, E.275, V.276, H.277, R.278, L.279 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:S.221, C:D.224, C:L.256, C:L.256, C:H.277, C:R.278 Salt bridges: C:R.49, C:R.49, C:R.49, C:R.131, C:K.149, C:K.149, C:K.149, C:R.278

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.3: 15 residues within 4Å: Chain C: M.64, T.66, T.68, D.69, K.106, P.107, L.108, V.109, K.128, I.129, H.130, R.131, L.132, P.133, K.222 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:T.68, C:T.68, C:D.69, C:K.106, C:V.109, C:V.109, C:H.130 Salt bridges: C:H.130, C:H.130, C:R.131, C:K.222, C:K.222

1 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.4: 13 residues within 4Å: Chain C: H.130, T.179, N.182, I.183, A.184, R.203, V.204, S.205, A.206, H.277, I.291, S.293, S.295 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:T.179, C:A.184, C:A.184, C:S.205, C:S.293, C:S.295 Salt bridges: C:H.130, C:H.277

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yan, Y. et al., Structure of an AMPK complex in an inactive, ATP-bound state. Science (2021)

Release Date

2021-07-21

Peptides

5'-AMP-activated protein kinase catalytic subunit alpha-1: A
5'-AMP-activated protein kinase subunit beta-2: B
5'-AMP-activated protein kinase subunit gamma-1: C
Maltodextrin-binding protein: D
Fab light chain: E
Fab heavy chain: F
Nanobody: G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
G

D
M

E
L

F
H

G
N

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

5'-AMP-activated protein kinase subunit beta-2

5'-AMP-activated protein kinase subunit gamma-1

Maltodextrin-binding protein

Fab light chain

Fab heavy chain

Nanobody

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