SMTL ID : 4bg4.1 (1 other biounit)

Crystal structure of Litopenaeus vannamei arginine kinase in a ternary analog complex with arginine, ADP-Mg and NO3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

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

ADP.1: 20 residues within 4Å: Chain A: S.122, T.123, 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: NO3.3, MG.4 25 PLIP interactions: 25 interactions with chain A Hydrogen bonds: A:S.122, A:R.280, A:S.282, A:H.284, A:T.311, A:E.314 Water bridges: A:R.124, A:H.185, A:H.185, A:L.187, A:R.229, A:R.229, A:R.229, A:S.282, A:R.312, A:G.313, A:D.324 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 ARG: ARGININE(Non-covalent)

ARG.2: 12 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 Ligands: NO3.3 14 PLIP interactions: 13 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:G.64, A:V.65, A:G.66, A:Y.68, A:T.273, A:N.274 Water bridges: A:I.67, A:D.192, A:E.225, A:R.309, A:R.309, R.2 Salt bridges: A:E.225, A:E.314

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

NO3.3: 9 residues within 4Å: Chain A: R.126, E.225, R.229, N.274, R.309, E.314 Ligands: ADP.1, ARG.2, MG.4 9 PLIP interactions: 8 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:R.126, A:E.225, A:R.229, A:R.229, A:N.274, A:R.309, A:R.309, R.2 Water bridges: A:R.330

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

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

1 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.5: 4 residues within 4Å: Chain A: L.46, D.52, P.138, C.139 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.52 Water bridges: A:D.52

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lopez-Zavala, A.A. et al., Crystal Structure of Shrimp Arginine Kinase in Binary Complex with Arginine-A Molecular View of the Phosphagen Precursor Binding to the Enzyme. J.Bioenerg.Biomembr. (2013)

Release Date

2013-09-04

Peptides

ARGININE KINASE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

ARGININE KINASE