SMTL ID : 4l6d.4 (3 other biounits)

Crystal structure of 5-carboxyvanillate decarboxylase from Sphingomonas paucimobilis complexed with vanillic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.45 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: VNL.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.16 MN.5: 4 residues within 4Å: Chain B: E.8, H.174, D.297 Ligands: VNL.6 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.8, B:H.174, B:D.297, H2O.33

5 x VNL: 4-HYDROXY-3-METHOXYBENZOATE(Non-covalent)

VNL.2: 11 residues within 4Å: Chain A: L.35, R.46, T.77, A.78, H.174, S.193, Y.198, D.297, Y.300 Chain B: N.245 Ligands: MN.1 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.300 Hydrogen bonds: A:S.193, B:N.245 Water bridges: A:R.46, A:R.46, A:A.78 Salt bridges: A:R.46 pi-Stacking: A:Y.198, A:Y.300 VNL.3: 7 residues within 4Å: Chain A: L.236, W.237, D.240, S.260, R.264, V.286 Chain B: S.276 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.236, A:W.237 Hydrogen bonds: A:D.240, A:D.240, A:S.260 Water bridges: A:R.264, A:R.264, B:S.276, B:H.277 pi-Stacking: A:W.237 VNL.6: 11 residues within 4Å: Chain A: N.245 Chain B: L.35, R.46, T.77, A.78, H.174, S.193, Y.198, D.297, Y.300 Ligands: MN.5 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.300 Hydrogen bonds: B:T.77, B:S.193, A:N.245 Water bridges: B:R.46, B:R.46, B:A.78 Salt bridges: B:R.46 pi-Stacking: B:Y.198, B:Y.300 VNL.7: 1 residues within 4Å: Chain B: R.127 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.127 Water bridges: B:R.127, B:R.127 Salt bridges: B:R.127 pi-Cation interactions: B:R.127 VNL.8: 7 residues within 4Å: Chain A: S.276 Chain B: L.236, W.237, D.240, S.260, R.264, V.286 11 PLIP interactions: 9 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.236, B:W.237 Hydrogen bonds: B:D.240, B:D.240, B:S.260 Water bridges: B:R.264, B:R.264, B:R.264, A:S.276, A:H.277 pi-Stacking: B:W.237

2 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.4: 5 residues within 4Å: Chain A: Y.241, M.242, H.243, G.244, N.245 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:M.242, A:G.244, A:N.245 EPE.9: 4 residues within 4Å: Chain B: Y.241, M.242, G.244, N.245 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:M.242, B:G.244, B:N.245

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

PEG.10: 2 residues within 4Å: Chain B: P.47, A.48 No protein-ligand interaction detected (PLIP)

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 vanillic acid. To be Published

Release Date

2013-11-13

Peptides

5-carboxyvanillate decarboxylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

5-carboxyvanillate decarboxylase

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