SMTL ID : 3n29.1

Crystal structure of carboxynorspermidine decarboxylase complexed with Norspermidine from Campylobacter jejuni

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

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

PLP.1: 13 residues within 4Å: Chain A: A.75, K.77, H.200, H.202, G.237, G.238, E.269, P.270, G.271, E.272, Y.378 Chain B: C.349 Ligands: NSD.2 13 PLIP interactions: 12 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:A.75, A:K.77, A:H.202 Hydrogen bonds: A:K.77, A:G.237, A:G.238, A:G.271, A:E.272, A:Y.378, B:C.349 Water bridges: A:H.239 Salt bridges: A:H.202 pi-Stacking: A:H.202 PLP.4: 12 residues within 4Å: Chain A: C.349 Chain B: A.75, K.77, H.200, H.202, G.237, G.238, E.269, P.270, G.271, E.272, Y.378 15 PLIP interactions: 14 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:A.75, B:K.77, B:H.202 Hydrogen bonds: B:G.237, B:G.238, B:E.269, B:G.271, B:E.272, B:Y.378 Water bridges: B:L.204, B:H.239, B:E.272, A:C.349 Salt bridges: B:H.202 pi-Stacking: B:H.202

1 x NSD: N-(3-AMINOPROPYL)PROPANE-1,3-DIAMINE(Non-covalent)

NSD.2: 8 residues within 4Å: Chain A: C.205, E.272, D.308, Y.378, K.382 Chain B: L.350, F.386 Ligands: PLP.1 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:L.350, B:F.386, A:Y.378 Hydrogen bonds: A:E.272, A:D.308, A:Y.378

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: D.308, Y.314, D.374, Q.375, H.377, Y.378, T.379 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.308, A:D.308, A:Y.314, A:D.374 Water bridges: A:Q.375 GOL.5: 7 residues within 4Å: Chain B: D.308, Y.314, D.374, Q.375, H.377, Y.378, T.379 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.308, B:D.374 Water bridges: B:Q.375

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

Carboxynorspermidine decarboxylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Carboxynorspermidine decarboxylase