SMTL ID : 5dzc.1

Crystal structure of the cGMP-dependent protein kinase PKG from Plasmodium Vivax - AMPPNP bound

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

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

ANP.1: 17 residues within 4Å: Chain A: I.541, G.542, G.544, V.549, A.562, K.564, I.596, T.612, E.613, L.614, V.615, E.619, L.665, I.675, D.676, A.817 Ligands: NA.6 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:K.564, A:T.612, A:E.613, A:V.615, A:E.619, A:D.676, A:D.676 Salt bridges: A:K.564 ANP.13: 17 residues within 4Å: Chain B: I.541, G.542, G.544, V.549, A.562, K.564, I.596, T.612, E.613, L.614, V.615, E.619, L.665, I.675, D.676, A.817 Ligands: NA.18 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:K.564, B:T.612, B:E.613, B:V.615, B:E.619, B:E.619, B:D.676 Salt bridges: B:K.564

14 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) UNX.7: 1 residues within 4Å: Chain A: Y.474 No protein-ligand interaction detected (PLIP) UNX.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) UNX.9: 3 residues within 4Å: Chain A: P.514, R.803, L.804 No protein-ligand interaction detected (PLIP) UNX.10: 3 residues within 4Å: Chain A: G.269, N.270, V.273 No protein-ligand interaction detected (PLIP) UNX.11: 1 residues within 4Å: Chain A: E.342 No protein-ligand interaction detected (PLIP) UNX.12: 2 residues within 4Å: Chain A: G.793, N.794 No protein-ligand interaction detected (PLIP) UNX.14: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) UNX.19: 1 residues within 4Å: Chain B: Y.474 No protein-ligand interaction detected (PLIP) UNX.20: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) UNX.21: 3 residues within 4Å: Chain B: P.514, R.803, L.804 No protein-ligand interaction detected (PLIP) UNX.22: 3 residues within 4Å: Chain B: G.269, N.270, V.273 No protein-ligand interaction detected (PLIP) UNX.23: 1 residues within 4Å: Chain B: E.342 No protein-ligand interaction detected (PLIP) UNX.24: 2 residues within 4Å: Chain B: G.793, N.794 No protein-ligand interaction detected (PLIP)

6 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 5 residues within 4Å: Chain A: G.446, S.447, R.448, Y.450, R.486 Ligand excluded by PLIP CL.4: 2 residues within 4Å: Chain A: E.176, A.177 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain A: A.305, I.306, V.307 Ligand excluded by PLIP CL.15: 5 residues within 4Å: Chain B: G.446, S.447, R.448, Y.450, R.486 Ligand excluded by PLIP CL.16: 2 residues within 4Å: Chain B: E.176, A.177 Ligand excluded by PLIP CL.17: 3 residues within 4Å: Chain B: A.305, I.306, V.307 Ligand excluded by PLIP

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

NA.6: 4 residues within 4Å: Chain A: E.662, N.663, D.676 Ligands: ANP.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.676, A:D.676 NA.18: 4 residues within 4Å: Chain B: E.662, N.663, D.676 Ligands: ANP.13 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.662

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

El Bakkouri, M. et al., Structures of the cGMP-dependent protein kinase in malaria parasites reveal a unique structural relay mechanism for activation. Proc.Natl.Acad.Sci.USA (2019)

Release Date

2015-10-14

Peptides

cGMP-dependent protein kinase, putative: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

cGMP-dependent protein kinase, putative

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