SMTL ID : 3h7k.1

Crystal Structure of Arabidopsis thaliana Agmatine Deiminase Complexed with a Covalently Bound Reaction Intermediate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.84 Å

Oligo State

monomer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: S.95, D.119, W.120, S.143 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.119, A:W.120, H2O.5, H2O.6, H2O.6

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

NA.2: 5 residues within 4Å: Chain A: W.125, D.130, E.219, D.220, N.222 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.130, A:N.185, A:N.222 NA.3: 1 residues within 4Å: Ligands: 1PE.8 No protein-ligand interaction detected (PLIP) NA.4: 3 residues within 4Å: Chain A: G.217, E.219, R.306 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.219

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

CL.5: 3 residues within 4Å: Chain A: P.300, L.302, T.305 Ligand excluded by PLIP CL.6: 1 residues within 4Å: Chain A: R.269 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain A: K.52, K.56 Ligand excluded by PLIP

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.8: 6 residues within 4Å: Chain A: Y.283, M.284, E.286, A.303, G.304 Ligands: NA.3 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.283

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Burgie, E.S. et al., Structural Insights into the Catalytic Mechanism of Arabidopsis thaliana Agmatine Deiminase. to be published

Release Date

2009-05-26

Peptides

Agmatine deiminase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Agmatine deiminase

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