SMTL ID : 4qrn.2 (1 other biounit)

HIGH-RESOLUTION CRYSTAL STRUCTURE of 5-CARBOXYVANILLATE DECARBOXYLASE (TARGET EFI-505250) FROM NOVOSPHINGOBIUM AROMATICIVORANS DSM 12444 COMPLEXED WITH MANGANESE AND 4-HYDROXY-3-METHOXY-5-NITROBENZOIC ACID

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.07 Å

Oligo State

homo-dimer

Ligands

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

MN.1: 5 residues within 4Å: Chain A: E.41, H.210, H.263, D.336 Ligands: 1DF.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.41, A:H.210, A:D.336, H2O.3 MN.7: 5 residues within 4Å: Chain B: E.41, H.210, H.263, D.336 Ligands: 1DF.8 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.41, B:H.210, B:D.336, H2O.22

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

1DF.2: 18 residues within 4Å: Chain A: E.41, L.69, W.70, Y.73, R.80, T.112, S.113, H.210, P.211, A.230, F.234, H.263, D.336, Y.339 Chain B: R.274, M.278, R.287 Ligands: MN.1 13 PLIP interactions: 10 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:A.230, A:F.234, A:Y.339, A:Y.339, A:Y.339 Hydrogen bonds: A:Y.73, A:T.112 Water bridges: A:S.113, A:A.230, B:R.287, B:R.287, B:R.287 Salt bridges: A:R.80 1DF.8: 18 residues within 4Å: Chain A: R.274, M.278, R.287 Chain B: E.41, L.69, W.70, Y.73, R.80, T.112, S.113, H.210, P.211, A.230, F.234, H.263, D.336, Y.339 Ligands: MN.7 13 PLIP interactions: 11 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:A.230, B:F.234, B:Y.339, B:Y.339, B:Y.339 Hydrogen bonds: B:Y.73, B:T.112 Water bridges: B:R.80, B:S.113, B:A.230, A:R.287, A:R.287 Salt bridges: B:R.80

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: D.63, H.182, Q.184, G.185, P.215, D.216 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Q.184, A:D.216, A:D.216 Water bridges: A:D.63, A:K.64, A:Q.184, A:Q.184, A:S.217 GOL.4: 5 residues within 4Å: Chain A: Y.277, Q.280, A.281, R.284 Chain B: R.80 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.281 Water bridges: A:Q.280 GOL.9: 7 residues within 4Å: Chain B: D.63, H.120, H.182, Q.184, G.185, P.215, D.216 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:D.63, B:D.216 Water bridges: B:K.64, B:H.120, B:H.120, B:Q.184, B:Q.184, B:D.216, B:D.216, B:S.217

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

CL.5: 5 residues within 4Å: Chain A: S.78, E.79, R.80 Chain B: R.284, S.285 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain A: E.190, E.191, R.290 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain B: Y.143, P.144, D.145, R.146 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain B: V.201, Y.254, P.255, S.256 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Patskovsky, Y. et al., Crystal Structure of 5-Carboxyvanillate Decarboxylase from Novosphingobium Aromaticivorans. To be Published

Release Date

2014-08-06

Peptides

5-Carboxyvanillate Decarboxylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

5-Carboxyvanillate Decarboxylase

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