SMTL ID : 4ng3.2 (3 other biounits)

Crystal structure of 5-carboxyvanillate decarboxylase from Sphingomonas paucimobilis complexed with 4-Hydroxy-3-methoxy-5-nitrobenzoic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 4 residues within 4Å: Chain A: E.8, H.174, D.297 Ligands: 1DF.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.8, A:H.174, A:D.297, H2O.10 MN.4: 4 residues within 4Å: Chain B: E.8, H.174, D.297 Ligands: 1DF.5 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.8, B:H.174, B:D.297, H2O.27

2 x 1DF: 4-hydroxy-3-methoxy-5-nitrobenzoic acid(Non-covalent)

1DF.2: 15 residues within 4Å: Chain A: E.8, L.35, R.46, T.77, A.78, H.174, S.193, A.194, Y.198, H.227, D.297, Y.300 Chain B: R.238, N.245 Ligands: MN.1 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:A.194, A:Y.300 Hydrogen bonds: A:S.193, B:N.245 Water bridges: A:R.46, A:R.46, A:A.78, A:S.193, A:Y.198 Salt bridges: A:R.46 pi-Stacking: A:Y.198, A:Y.300 1DF.5: 15 residues within 4Å: Chain A: R.238, N.245 Chain B: E.8, L.35, R.46, T.77, A.78, H.174, S.193, A.194, Y.198, H.227, D.297, Y.300 Ligands: MN.4 10 PLIP interactions: 1 interactions with chain A, 9 interactions with chain B Hydrogen bonds: A:N.245, B:S.193 Hydrophobic interactions: B:Y.300 Water bridges: B:R.46, B:A.78, B:S.193, B:Y.198 Salt bridges: B:R.46 pi-Stacking: B:Y.198, B:Y.300

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 4 residues within 4Å: Chain A: Y.241, M.242, G.244, N.245 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:M.242, A:G.244, A:N.245

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.6: 5 residues within 4Å: Chain B: Y.241, M.242, H.243, G.244, N.245 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:M.242, B:G.244, B:N.245 Water bridges: B:H.243

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fedorov, A.A. et al., Crystal structure of 5-carboxyvanillate decarboxylase from Sphingomonas paucimobilis complexed with 4-Hydroxy-3-methoxy-5-nitrobenzoic acid. To be Published

Release Date

2013-11-13

Peptides

5-carboxyvanillate decarboxylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
G

5-carboxyvanillate decarboxylase

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