SMTL ID : 6w54.1

Crystal Structure of Gallic Acid Decarboxylase from Arxula adeninivorans

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-trimer

Ligands

3 x 4NC: 4-NITROCATECHOL(Non-covalent)

4NC.1: 12 residues within 4Å: Chain A: W.35, R.39, T.59, T.60, W.61, I.84, H.86, I.110, Y.146, Y.150, L.188, Q.192 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:W.35, A:T.59, A:I.110 Hydrogen bonds: A:T.60, A:T.60, A:T.60, A:W.61, A:Y.150, A:Q.192 4NC.4: 12 residues within 4Å: Chain B: W.35, R.39, T.59, T.60, W.61, I.84, H.86, I.110, Y.146, Y.150, L.188, Q.192 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:W.35, B:T.59, B:I.110 Hydrogen bonds: B:T.60, B:T.60, B:T.60, B:W.61, B:Y.150, B:Q.192 4NC.7: 12 residues within 4Å: Chain C: W.35, R.39, T.59, T.60, W.61, I.84, H.86, I.110, Y.146, Y.150, L.188, Q.192 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:W.35, C:T.59, C:I.110 Hydrogen bonds: C:T.60, C:T.60, C:T.60, C:W.61, C:Y.150, C:Q.192

3 x K: POTASSIUM ION(Non-covalent)

K.2: 5 residues within 4Å: Chain A: E.88 Chain B: E.88 Chain C: E.88 Ligands: K.5, K.8 5 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C, 2 interactions with chain A Metal complexes: B:E.88, C:E.88, C:E.88, A:E.88, A:E.88 K.5: 5 residues within 4Å: Chain A: E.88 Chain B: E.88 Chain C: E.88 Ligands: K.2, K.8 5 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C, 2 interactions with chain A Metal complexes: B:E.88, C:E.88, C:E.88, A:E.88, A:E.88 K.8: 5 residues within 4Å: Chain A: E.88 Chain B: E.88 Chain C: E.88 Ligands: K.2, K.5 5 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C, 2 interactions with chain A Metal complexes: B:E.88, C:E.88, C:E.88, A:E.88, A:E.88

3 x CO: COBALT (II) ION(Non-covalent)

CO.3: 2 residues within 4Å: Chain A: E.49 Chain B: H.14 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.49, H2O.1, H2O.3, H2O.5, H2O.9 CO.6: 2 residues within 4Å: Chain B: E.49 Chain C: H.14 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:E.49, H2O.8, H2O.10, H2O.12, H2O.16 CO.9: 2 residues within 4Å: Chain A: H.14 Chain C: E.49 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:E.49, H2O.1, H2O.15, H2O.17, H2O.19

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zeug, M. et al., Crystal structures of non-oxidative decarboxylases reveal a new mechanism of action with a catalytic dyad and structural twists. Sci Rep (2021)

Release Date

2021-02-17

Peptides

Gallate decarboxylase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Gallate decarboxylase

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