SMTL ID : 7lv3.1

Crystal structure of human protein kinase G (PKG) R-C complex in inhibited state

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.41 Å

Oligo State

homo-dimer

Ligands

4 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 4 residues within 4Å: Chain A: D.430, D.448 Ligands: MN.2, ANP.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.448, A:D.448, H2O.1, H2O.2 MN.2: 4 residues within 4Å: Chain A: N.435, D.448 Ligands: MN.1, ANP.3 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.448, H2O.2 MN.5: 3 residues within 4Å: Chain B: D.430, D.448 Ligands: ANP.7 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.448, B:D.448, H2O.3 MN.6: 3 residues within 4Å: Chain B: N.435, D.448 Ligands: ANP.7 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.448

2 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.3: 25 residues within 4Å: Chain A: L.312, G.313, G.315, G.316, F.317, G.318, V.320, A.334, K.336, V.368, M.384, E.385, C.387, E.391, D.430, K.432, E.434, N.435, I.437, V.447, D.448, F.595 Chain B: A.9 Ligands: MN.1, MN.2 13 PLIP interactions: 11 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.316, A:F.317, A:G.318, A:K.336, A:E.385, A:C.387, A:E.391, A:K.432, B:A.9 Water bridges: A:E.434, A:N.435, B:K.6 Salt bridges: A:K.336 ANP.7: 25 residues within 4Å: Chain A: A.9 Chain B: L.312, G.313, G.315, G.316, F.317, V.320, A.334, K.336, V.368, M.384, E.385, A.386, C.387, E.391, D.430, K.432, E.434, N.435, I.437, V.447, D.448, F.595 Ligands: MN.5, MN.6 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.316, B:F.317, B:K.336, B:E.385, B:C.387, B:E.391, B:K.432, A:A.9 Water bridges: B:D.448, B:D.448 Salt bridges: B:K.336

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 5 residues within 4Å: Chain A: D.521, R.542, D.543, N.544, E.547 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.542, A:D.543, A:D.543, A:N.544, A:E.547 EDO.8: 2 residues within 4Å: Chain B: T.124, A.125 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.124, B:A.125 Water bridges: B:R.123 EDO.9: 3 residues within 4Å: Chain B: N.532, K.563, E.566 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.532, B:N.532, B:E.566, B:E.566

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sharma, R. et al., An auto-inhibited state of protein kinase G and implications for selective activation. Elife (2022)

Release Date

2022-08-24

Peptides

Isoform Beta of cGMP-dependent protein kinase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Isoform Beta of cGMP-dependent protein kinase 1