SMTL ID : 3n2o.1 (1 other biounit)

X-ray crystal structure of arginine decarboxylase complexed with Arginine from Vibrio vulnificus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x PLP: PYRIDOXAL-5'-PHOSPHATE(Covalent)

PLP.1: 15 residues within 4Å: Chain A: P.103, K.105, E.131, N.155, H.253, H.255, S.258, G.294, G.295, E.343, S.344, G.345, R.346, Y.551 Chain B: C.511 13 PLIP interactions: 1 interactions with chain B, 12 interactions with chain A Hydrogen bonds: B:C.511, A:S.258, A:G.294, A:G.295, A:G.345, A:R.346 Hydrophobic interactions: A:P.103, A:K.105 Water bridges: A:Q.259, A:Q.259, A:L.296, A:S.347 pi-Stacking: A:H.255 PLP.4: 17 residues within 4Å: Chain A: C.511 Chain B: P.103, K.105, V.106, E.131, N.155, H.253, H.255, S.258, G.294, G.295, E.343, S.344, G.345, R.346, Y.551 Ligands: AG2.2 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:K.105 Hydrogen bonds: B:S.258, B:Q.259, B:G.294, B:G.295, B:E.343, B:G.345, B:R.346, B:Y.551 Water bridges: B:S.347 pi-Stacking: B:H.255

2 x AG2: AGMATINE(Non-covalent)

AG2.2: 10 residues within 4Å: Chain A: W.482, D.512, S.513 Chain B: K.105, H.255, G.257, S.258, D.480, L.555 Ligands: PLP.4 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:S.513, B:S.258 Salt bridges: A:D.512, B:D.480 pi-Cation interactions: B:Y.551 AG2.3: 10 residues within 4Å: Chain A: K.105, H.255, G.257, S.258, Y.551, L.555 Chain B: F.475, W.482, D.512, S.513 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:W.482, B:S.513, B:S.513, A:S.258 Salt bridges: B:D.512, A:D.480

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Deng, X. et al., Evolution of substrate specificity within a diverse family of beta/alpha-barrel-fold basic amino acid decarboxylases: X-ray structure determination of enzymes with specificity for L-arginine and carboxynorspermidine. J.Biol.Chem. (2010)

Release Date

2010-06-09

Peptides

Biosynthetic arginine decarboxylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Biosynthetic arginine decarboxylase

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