SMTL ID : 6mo3.1

Citrobacter freundii tyrosine phenol-lyase complexed with 4-hydroxypyridine and aminoacrylate from L-serine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.79 Å

Oligo State

homo-tetramer

Ligands

6 x CQG: pyridin-4-ol(Non-covalent)

CQG.1: 3 residues within 4Å: Chain A: E.227, Q.228, R.323 No protein-ligand interaction detected (PLIP) CQG.2: 9 residues within 4Å: Chain A: R.100, F.123, T.124, M.379, R.381, F.448, F.449 Chain B: Y.71 Ligands: 0JO.3 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.123, A:F.448 Hydrogen bonds: A:R.100, A:T.124, A:R.381, A:R.381 pi-Stacking: A:F.449 CQG.6: 8 residues within 4Å: Chain A: D.68, E.75 Chain B: E.14, T.15, V.16, S.40, K.41 Chain C: R.9 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.68 Water bridges: B:S.17 CQG.9: 3 residues within 4Å: Chain C: E.227, Q.228, R.323 No protein-ligand interaction detected (PLIP) CQG.10: 9 residues within 4Å: Chain C: R.100, F.123, T.124, M.379, R.381, F.448, F.449 Chain D: Y.71 Ligands: 0JO.11 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:F.123, C:F.448 Hydrogen bonds: C:R.100, C:R.381, C:R.381 pi-Stacking: C:F.449 CQG.14: 8 residues within 4Å: Chain A: R.9 Chain C: D.68, E.75 Chain D: E.14, T.15, V.16, S.40, K.41 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:D.68, D:E.14 Water bridges: D:S.17

2 x 0JO: 2-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}prop-2-enoic acid(Non-covalent)

0JO.3: 19 residues within 4Å: Chain A: T.49, S.51, Q.98, G.99, R.100, E.103, F.123, T.125, N.185, D.214, T.216, R.217, S.254, K.256, K.257, M.379, R.404 Chain B: Y.71 Ligands: CQG.2 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:T.49, A:S.51, A:S.51, A:Q.98, A:G.99, A:R.100, A:N.185, A:T.216, A:R.217, A:R.217, A:S.254, A:K.257 Water bridges: A:T.126, A:K.256 Salt bridges: A:R.100, A:R.217, A:K.256, A:K.257, A:K.257, A:R.404 pi-Stacking: A:F.123 0JO.11: 19 residues within 4Å: Chain C: T.49, S.51, Q.98, G.99, R.100, E.103, F.123, T.125, N.185, D.214, T.216, R.217, S.254, K.256, K.257, M.379, R.404 Chain D: Y.71 Ligands: CQG.10 20 PLIP interactions: 19 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:S.51, C:S.51, C:Q.98, C:G.99, C:R.100, C:N.185, C:R.217, C:R.217, C:S.254, C:K.257 Water bridges: C:T.216, C:K.256, D:Y.71 Salt bridges: C:R.100, C:R.217, C:K.256, C:K.257, C:K.257, C:R.404 pi-Stacking: C:F.123

4 x K: POTASSIUM ION(Non-covalent)

K.4: 3 residues within 4Å: Chain A: G.52, N.262 Chain B: E.69 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:G.52, A:N.262, B:E.69, H2O.4, H2O.14 K.5: 3 residues within 4Å: Chain A: E.69 Chain B: G.52, N.262 5 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:E.69, B:G.52, B:N.262, H2O.3, H2O.5 K.12: 3 residues within 4Å: Chain C: G.52, N.262 Chain D: E.69 5 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: C:G.52, C:N.262, D:E.69, H2O.29, H2O.38 K.13: 3 residues within 4Å: Chain C: E.69 Chain D: G.52, N.262 5 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: D:G.52, D:N.262, C:E.69, H2O.28, H2O.29

2 x SER: SERINE(Covalent)

SER.7: 9 residues within 4Å: Chain A: Y.71 Chain B: T.49, S.51, R.100, F.123, N.185, R.217, K.257, R.404 7 PLIP interactions: 5 interactions with chain B, 1 Ligand-Ligand interactions, 1 interactions with chain A Hydrogen bonds: B:T.49, B:R.100, B:N.185, B:R.217, S.7, A:Y.71 Salt bridges: B:R.404 SER.15: 9 residues within 4Å: Chain C: Y.71 Chain D: T.49, S.51, R.100, F.123, N.185, R.217, K.257, R.404 8 PLIP interactions: 5 interactions with chain D, 2 interactions with chain C, 1 Ligand-Ligand interactions Hydrogen bonds: D:T.49, D:R.100, D:N.185, D:R.217, C:Y.71, C:Y.71, S.15 Salt bridges: D:R.404

2 x P33: 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL(Non-covalent)

P33.8: 13 residues within 4Å: Chain B: Y.3, A.5, Y.324, Y.414, A.415, D.418 Chain C: Y.3, A.5, Y.324, Y.414, A.415, D.418, D.422 1 PLIP interactions: 1 interactions with chain B Water bridges: B:A.5 P33.16: 13 residues within 4Å: Chain A: Y.3, A.5, Y.324, Y.414, A.415, D.418, D.422 Chain D: Y.3, A.5, Y.324, Y.414, A.415, D.418 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:Y.324, D:D.418 Water bridges: D:A.5, D:D.422, A:D.422

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Phillips, R.S. et al., Pressure and Temperature Effects on the Formation of Aminoacrylate Intermediates of Tyrosine Phenol-lyase Demonstrate Reaction Dynamics. Acs Catalysis (2020)

Release Date

2019-10-16

Peptides

Tyrosine phenol-lyase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Tyrosine phenol-lyase

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