SMTL ID : 5jix.1

PKG II's Carboxyl Terminal Cyclic Nucleotide Binding Domain (CNB-B) in a complex with 8-Br-cGMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.47 Å

Oligo State

monomer

Ligands

4 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.1: 3 residues within 4Å: Chain A: K.81, T.82, L.83 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.82, H2O.1, H2O.2, H2O.4 CA.2: 1 residues within 4Å: Chain A: N.141 No protein-ligand interaction detected (PLIP) CA.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.4: 2 residues within 4Å: Chain A: E.129, Q.132 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.129, H2O.3

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

EDO.5: 7 residues within 4Å: Chain A: Y.46, I.47, I.48, R.49, E.52 Ligands: EDO.7, NA.12 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.49, A:E.52 EDO.6: 6 residues within 4Å: Chain A: K.31, C.35, D.117, E.119, T.120, Q.123 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.31, A:T.120 Water bridges: A:D.117, A:D.117 EDO.7: 12 residues within 4Å: Chain A: I.47, I.48, R.49, E.52, E.53, G.54, S.55, T.56, F.58, R.100 Ligands: EDO.5, NA.12 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.56, A:T.56, A:R.100, A:R.100 Water bridges: A:T.56 EDO.8: 4 residues within 4Å: Chain A: Y.40, Y.41, D.42, D.45 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.45 EDO.9: 4 residues within 4Å: Chain A: L.83, E.87, Y.88, Y.138 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.88 Water bridges: A:S.19, A:E.87, A:E.87, A:Y.138

1 x PE5: 3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL(Non-covalent)

PE5.10: 9 residues within 4Å: Chain A: K.43, G.44, K.66, T.68, L.79, T.82, I.105, A.106, E.107 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.66

1 x 6J7: 2-amino-8-bromo-9-[(2R,4aR,6R,7R,7aS)-2,7-dihydroxy-2-oxotetrahydro-2H,4H-2lambda~5~-furo[3,2-d][1,3,2]dioxaphosphinin-6-yl]-1,9-dihydro-6H-purin-6-one(Non-covalent)

6J7.11: 20 residues within 4Å: Chain A: I.48, V.67, Q.69, I.80, K.81, L.83, F.89, G.90, E.91, K.92, A.93, R.100, S.101, A.102, I.104, Y.138, L.142, D.145, D.146, R.149 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:Q.69, A:K.81, A:G.90, A:E.91, A:E.91, A:K.92, A:A.93, A:S.101, A:S.101, A:S.101, A:S.101, A:R.149, A:R.149 Water bridges: A:Y.138 Salt bridges: A:R.100, A:D.146

1 x NA: SODIUM ION(Non-functional Binders)

NA.12: 6 residues within 4Å: Chain A: E.39, Y.41, I.47, F.58 Ligands: EDO.5, EDO.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.47

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Campbell, J.C. et al., Structural Basis of Analog Specificity in PKG I and II. ACS Chem. Biol. (2017)

Release Date

2017-05-03

Peptides

cGMP-dependent protein kinase 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

cGMP-dependent protein kinase 2

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