SMTL ID : 7tdl.1

M379A mutant tyrosine phenol-lyase complexed with 3-bromo-DL-phenylalanine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-tetramer

Ligands

4 x K: POTASSIUM ION(Non-covalent)

K.1: 6 residues within 4Å: Chain A: G.52, K.256, N.262 Chain B: E.69, A.295, G.296 5 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:E.69, A:G.52, A:N.262, H2O.5, H2O.16 K.2: 5 residues within 4Å: Chain A: E.69, A.295, G.296 Chain B: G.52, N.262 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:G.52, B:N.262, A:E.69, H2O.2, H2O.3 K.9: 5 residues within 4Å: Chain C: G.52, N.262 Chain D: E.69, A.295, G.296 5 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: D:E.69, C:G.52, C:N.262, H2O.44, H2O.46 K.10: 5 residues within 4Å: Chain C: E.69, A.295, G.296 Chain D: G.52, N.262 5 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: C:E.69, D:G.52, D:N.262, H2O.28, H2O.32

2 x OY3: (4Z)-4-({[(1E)-2-(3-bromophenyl)-1-carboxyethylidene]azaniumyl}methylidene)-2-methyl-5-[(phosphonooxy)methyl]-1,4-dihydropyridin-3-olate(Non-covalent)

OY3.3: 24 residues within 4Å: Chain A: F.36, T.49, S.51, Q.98, G.99, R.100, E.103, F.123, T.124, T.125, T.126, A.181, N.185, D.214, T.216, R.217, S.254, K.256, K.257, R.381, R.404, F.448 Chain B: Y.71, M.288 22 PLIP interactions: 21 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.123, A:F.448, B:Y.71 Hydrogen bonds: A:T.49, A:S.51, A:Q.98, A:G.99, A:R.100, A:N.185, A:D.214, A:R.217, A:R.217, A:K.257 Water bridges: A:T.216, 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 OY3.6: 26 residues within 4Å: Chain A: Y.71, V.283, M.288 Chain B: F.36, T.49, S.51, Q.98, G.99, R.100, E.103, F.123, T.124, T.125, T.126, A.181, N.185, D.214, T.216, R.217, S.254, K.256, K.257, R.404, F.448 Ligands: DMS.4, PLP.7 25 PLIP interactions: 24 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.123, A:Y.71 Hydrogen bonds: B:T.49, B:Q.98, B:G.99, B:R.100, B:N.185, B:D.214, B:R.217, B:R.217, B:S.254, B:S.254, B:K.257 Water bridges: B:S.51, B:T.216, B:K.256, B:R.404, B:R.404 Salt bridges: B:R.100, B:R.217, B:K.256, B:K.257, B:K.257, B:R.404 pi-Stacking: B:F.123

4 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.4: 7 residues within 4Å: Chain A: V.283, V.284 Chain B: T.124, T.125, Y.128, L.446 Ligands: OY3.6 No protein-ligand interaction detected (PLIP) DMS.8: 8 residues within 4Å: Chain A: K.11, S.12, D.58, W.61 Chain B: M.65 Chain C: K.11, S.12, W.61 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:S.12, C:S.12 pi-Cation interactions: A:W.61, C:W.61, C:W.61 DMS.11: 2 residues within 4Å: Chain C: A.206, H.207 No protein-ligand interaction detected (PLIP) DMS.14: 8 residues within 4Å: Chain A: M.65 Chain B: K.11, S.12, D.58, W.61 Chain D: K.11, S.12, W.61 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:S.12 pi-Cation interactions: D:W.61, D:W.61, B:W.61

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

CL.5: 6 residues within 4Å: Chain A: T.124, T.125, Y.128, L.446 Chain B: V.283, V.284 Ligand excluded by PLIP CL.13: 6 residues within 4Å: Chain C: F.36, F.123, R.381, R.404, F.448, F.449 Ligand excluded by PLIP CL.16: 6 residues within 4Å: Chain D: F.36, F.123, R.381, R.404, F.448, F.449 Ligand excluded by PLIP

3 x PLP: PYRIDOXAL-5'-PHOSPHATE(Covalent)

PLP.7: 16 residues within 4Å: Chain B: S.51, Q.98, G.99, R.100, E.103, F.123, T.125, T.126, N.185, D.214, T.216, R.217, S.254, K.256, K.257 Ligands: OY3.6 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:F.123, B:N.185, B:K.257 Hydrogen bonds: B:Q.98, B:G.99, B:R.100, B:N.185, B:D.214, B:R.217, B:R.217, B:S.254, B:K.257 Water bridges: B:S.51, B:S.51 Salt bridges: B:R.100, B:K.256, B:K.257 pi-Stacking: B:F.123 PLP.12: 16 residues within 4Å: Chain C: S.51, Q.98, G.99, R.100, E.103, F.123, T.125, T.126, A.181, N.185, D.214, T.216, R.217, S.254, K.256, K.257 19 PLIP interactions: 18 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:F.123, C:F.123, C:K.257 Hydrogen bonds: C:Q.98, C:G.99, C:R.100, C:T.216, C:R.217, C:R.217, C:S.254 Water bridges: C:S.51, C:S.51, C:S.51, C:R.100, C:E.103, D:Y.71 Salt bridges: C:R.100, C:K.257 pi-Stacking: C:F.123 PLP.15: 17 residues within 4Å: Chain C: Y.71 Chain D: S.51, Q.98, G.99, R.100, E.103, F.123, T.125, T.126, A.181, N.185, D.214, T.216, R.217, S.254, K.256, K.257 18 PLIP interactions: 16 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:F.123, D:F.123, D:K.257 Hydrogen bonds: D:S.51, D:Q.98, D:G.99, D:R.100, D:R.217, D:R.217, D:S.254 Water bridges: D:E.103, D:K.256, C:Y.71, C:Y.71 Salt bridges: D:R.100, D:K.256, D:K.257 pi-Stacking: D:F.123

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Phillips, R.S. et al., M379A Mutant Tyrosine Phenol-lyase from Citrobacter freundii Has Altered Conformational Dynamics. Chembiochem (2022)

Release Date

2022-06-01

Peptides

Tyrosine phenol-lyase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Tyrosine phenol-lyase

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