SMTL ID : 4gvz.1

Crystal structure of arginine kinase in complex with D-arginine, MgADP, and nitrate.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.96 Å

Oligo State

monomer

Ligands

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

ADP.1: 19 residues within 4Å: Chain A: S.122, R.124, R.126, H.185, W.221, R.229, M.233, R.280, S.282, V.283, H.284, R.309, T.311, R.312, G.313, E.314, D.324 Ligands: MG.2, NO3.3 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:S.122, A:R.124, A:R.280, A:S.282, A:R.312, A:E.314 Water bridges: A:R.124, A:R.229, A:S.282 Salt bridges: A:R.124, A:R.126, A:R.229, A:R.280, A:R.280, A:R.309, A:R.309 pi-Stacking: A:H.284

1 x MG: MAGNESIUM ION(Non-functional Binders)

MG.2: 2 residues within 4Å: Ligands: ADP.1, NO3.3 No protein-ligand interaction detected (PLIP)

1 x NO3: NITRATE ION(Non-functional Binders)

NO3.3: 8 residues within 4Å: Chain A: R.126, R.229, N.274, R.309, E.314 Ligands: ADP.1, MG.2, DAR.4 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:R.126, A:R.229, A:R.229, A:N.274, A:R.309, A:R.309 Water bridges: A:E.225, A:T.273, A:T.273, A:E.314, A:E.314

1 x DAR: D-ARGININE(Non-covalent)

DAR.4: 13 residues within 4Å: Chain A: S.63, G.64, V.65, G.66, Y.68, F.194, E.225, C.271, T.273, N.274, E.314, H.315 Ligands: NO3.3 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:G.64, A:V.65, A:G.66, A:Y.68, A:Y.68, A:T.273, A:T.273, A:N.274 Water bridges: A:S.63, A:R.309, A:E.314, A:E.314 Salt bridges: A:E.225, A:E.314, A:H.315

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Clark, S.A. et al., Crystal structures of arginine kinase in complex with ADP, nitrate, and various phosphagen analogs. Biochem.Biophys.Res.Commun. (2012)

Release Date

2012-10-03

Peptides

Arginine kinase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Arginine kinase

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