SMTL ID : 1m15.1

Transition state structure of arginine kinase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.20 Å

Oligo State

monomer

Ligands

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

NO3.1: 6 residues within 4Å: Chain A: G.112, L.113, D.114, P.115, G.237, D.238 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.112, A:L.113, A:D.114, A:G.237 NO3.2: 9 residues within 4Å: Chain A: R.126, E.225, R.229, N.274, R.309, E.314 Ligands: MG.3, ARG.4, ADP.5 9 PLIP interactions: 1 Ligand-Ligand interactions, 8 interactions with chain A Hydrogen bonds: R.4, A:R.126, A:E.225, A:R.229, A:R.229, A:N.274, A:R.309, A:R.309 Water bridges: A:R.330

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

MG.3: 2 residues within 4Å: Ligands: NO3.2, ADP.5 No protein-ligand interaction detected (PLIP)

1 x ARG: ARGININE(Non-covalent)

ARG.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: NO3.2 18 PLIP interactions: 1 Ligand-Ligand interactions, 17 interactions with chain A Water bridges: R.4, A:D.62, A:I.67, A:Y.68, A:E.225, A:R.309, A:R.309, A:H.315, A:H.315 Hydrogen bonds: A:G.64, A:V.65, A:G.66, A:Y.68, A:T.273, A:N.274 Salt bridges: A:E.225, A:E.314, A:H.315

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

ADP.5: 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: NO3.2, MG.3 23 PLIP interactions: 20 interactions with chain A, 3 Ligand-Ligand interactions 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:L.187, A:R.229, A:R.229, A:S.282, A:R.312, R.4, R.4, R.4 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yousef, M.S. et al., Refinement of the arginine kinase transition-state analogue complex at 1.2 A resolution: mechanistic insights. Acta Crystallogr.,Sect.D (2002)

Release Date

2002-12-04

Peptides

arginine kinase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

arginine kinase

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