SMTL ID : 6ecg.1

Citrobacter freundii tyrosine phenol-lyase F448A mutant complexed with L-methionine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.27 Å

Oligo State

homo-tetramer

Ligands

4 x K: POTASSIUM ION(Non-covalent)

K.1: 3 residues within 4Å: Chain A: G.51, N.261 Chain B: E.68 5 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:E.68, A:G.51, A:N.261, H2O.13, H2O.16 K.2: 3 residues within 4Å: Chain A: E.68 Chain B: G.51, N.261 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:E.68, B:G.51, H2O.3, H2O.5, H2O.16 K.6: 3 residues within 4Å: Chain C: G.51, N.261 Chain D: E.68 5 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: D:E.68, C:G.51, C:N.261, H2O.38, H2O.41 K.7: 3 residues within 4Å: Chain C: E.68 Chain D: G.51, N.261 5 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: D:G.51, C:E.68, H2O.28, H2O.30, H2O.41

2 x PM9: (2E)-2-{[(Z)-{3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4(1H)-YLIDENE}METHYL]IMINO}-4-(METHYLSULFANYL)BUTANOIC ACID

PM9.3: 20 residues within 4Å: Chain A: T.48, S.50, Q.97, G.98, R.99, E.102, F.122, T.124, T.125, N.184, D.213, T.215, R.216, S.253, K.255, K.256, M.378, R.380, R.403 Chain B: Y.70 21 PLIP interactions: 20 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:T.48, A:S.50, A:Q.97, A:G.98, A:R.99, A:T.125, A:N.184, A:D.213, A:T.215, A:R.216, A:R.216, A:S.253, A:K.256 Water bridges: A:K.255, B:Y.290 Salt bridges: A:R.99, A:R.216, A:K.256, A:K.256, A:R.403 pi-Stacking: A:F.122 PM9.8: 20 residues within 4Å: Chain C: T.48, S.50, Q.97, G.98, R.99, E.102, F.122, T.124, T.125, N.184, D.213, T.215, R.216, S.253, K.255, K.256, M.378, R.380, R.403 Chain D: Y.70 20 PLIP interactions: 19 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:T.48, C:S.50, C:Q.97, C:G.98, C:R.99, C:N.184, C:D.213, C:R.216, C:R.216, C:S.253, C:K.256 Water bridges: C:E.102, C:K.255, D:Y.290 Salt bridges: C:R.99, C:R.216, C:K.256, C:K.256, C:R.403 pi-Stacking: C:F.122

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.4: 3 residues within 4Å: Chain A: K.225, E.232, Y.311 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.225 Water bridges: A:Y.311 PGE.9: 3 residues within 4Å: Chain C: K.225, E.232, Y.311 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.225 Water bridges: C:Y.311

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

P33.5: 12 residues within 4Å: Chain A: Y.2, A.4, Y.323, Y.413, A.414, D.417 Chain D: Y.2, A.4, Y.323, Y.413, A.414, D.417 7 PLIP interactions: 1 interactions with chain A, 6 interactions with chain D Hydrogen bonds: A:Y.323, D:Y.323, D:D.417 Water bridges: D:A.4, D:A.4, D:D.421, D:D.421 P33.10: 12 residues within 4Å: Chain B: Y.2, A.4, Y.323, Y.413, A.414, D.417 Chain C: Y.2, A.4, Y.323, Y.413, A.414, D.417 3 PLIP interactions: 3 interactions with chain B Water bridges: B:A.4, B:A.4, B:D.421

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Phillips, R.S. et al., Crystal Structures of Wild-Type and F448A Mutant Citrobacter freundii Tyrosine Phenol-Lyase Complexed with a Substrate and Inhibitors: Implications for the Reaction Mechanism. Biochemistry (2018)

Release Date

2018-10-10

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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