SMTL ID : 4ofg.1

Co-crystal structure of carboxy cGMP binding domain of Plasmodium falciparum PKG with cGMP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x PCG: CYCLIC GUANOSINE MONOPHOSPHATE(Non-covalent)

PCG.1: 15 residues within 4Å: Chain A: I.67, L.74, R.75, F.83, G.84, E.85, R.86, A.87, R.94, T.95, A.96, V.98, Q.134, V.138 Ligands: EOH.22 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:R.75, A:G.84, A:E.85, A:E.85, A:R.86, A:A.87, A:T.95, A:T.95, A:T.95, A:Q.134 Water bridges: A:R.86 Salt bridges: A:R.94 pi-Cation interactions: A:R.86

6 x N2P: PENTANE-1,5-DIAMINE(Non-covalent)

N2P.2: 4 residues within 4Å: Chain A: D.81, Y.82, R.130, Q.134 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:D.81, A:Y.82, A:Y.82 Hydrogen bonds: A:D.81, A:Y.82, A:Q.134 N2P.3: 4 residues within 4Å: Chain A: T.76, L.77, D.81 Ligands: N2P.5 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.77 N2P.4: 4 residues within 4Å: Chain A: A.4, D.7, K.11, E.34 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:A.4, A:D.7 Hydrogen bonds: A:D.7, A:D.7, A:I.33 Water bridges: A:K.11 N2P.5: 5 residues within 4Å: Chain A: R.75, R.130, M.133, Q.134 Ligands: N2P.3 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:R.130 Hydrogen bonds: A:Q.134 N2P.6: 6 residues within 4Å: Chain A: L.88, L.89, D.91, K.112, L.116, Q.120 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.116 Hydrogen bonds: A:K.112, A:K.112, A:Q.120 N2P.7: 2 residues within 4Å: Chain A: S.113, Q.117 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.117

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.8: 6 residues within 4Å: Chain A: G.54, S.55, R.56, Y.58, R.94 Ligands: EOH.14 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.55, A:R.56, A:Y.58, A:Y.58 Water bridges: A:R.94 Salt bridges: A:R.56, A:R.94 SO4.9: 5 residues within 4Å: Chain A: Y.19, R.22, H.126, R.130 Ligands: EOH.11 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:R.22, A:H.126, A:R.130 SO4.10: 4 residues within 4Å: Chain A: K.11, F.36, R.37, T.38 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.38 Salt bridges: A:K.11

13 x EOH: ETHANOL(Non-functional Binders)

EOH.11: 5 residues within 4Å: Chain A: I.20, R.22, Y.23, M.123 Ligands: SO4.9 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.23 Hydrogen bonds: A:R.22 EOH.12: 3 residues within 4Å: Chain A: Y.8, D.26, C.29 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.8, A:Y.8 EOH.13: 2 residues within 4Å: Chain A: K.27, Q.117 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.27 Water bridges: A:Q.117 EOH.14: 6 residues within 4Å: Chain A: T.39, Y.41, R.56, Y.58, F.109 Ligands: SO4.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.58 EOH.15: 3 residues within 4Å: Chain A: Y.46, Q.49, E.52 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Q.49 Water bridges: A:E.52 EOH.16: 4 residues within 4Å: Chain A: K.69, N.70, L.74 Ligands: EOH.17 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:N.70 EOH.17: 5 residues within 4Å: Chain A: K.69, N.70, K.72, V.138 Ligands: EOH.16 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:N.70 EOH.18: 2 residues within 4Å: Chain A: Y.19, R.22 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.19, A:Y.19 EOH.19: 2 residues within 4Å: Chain A: R.75, T.76 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.76 EOH.20: 2 residues within 4Å: Chain A: T.39, R.40 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:R.40 Hydrogen bonds: A:R.40, A:R.40 EOH.21: 3 residues within 4Å: Chain A: Y.46, V.68, I.99 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.68 EOH.22: 4 residues within 4Å: Chain A: K.69, R.86, D.135 Ligands: PCG.1 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:K.69 Hydrogen bonds: A:R.86, A:R.86, A:D.135 EOH.23: 6 residues within 4Å: Chain A: A.35, R.37, R.56, F.109, V.110, D.111 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:R.37 Hydrogen bonds: A:R.56, A:R.56

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, J.J. et al., Crystal Structures of the Carboxyl cGMP Binding Domain of the Plasmodium falciparum cGMP-dependent Protein Kinase Reveal a Novel Capping Triad Crucial for Merozoite Egress. Plos Pathog. (2015)

Release Date

2015-01-21

Peptides

CGMP-dependent protein kinase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

CGMP-dependent protein kinase

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