SMTL ID : 7tcs.1

M379A mutant tyrosine phenol-lyase complexed with L-methionine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.37 Å

Oligo State

homo-tetramer

Ligands

4 x K: POTASSIUM ION(Non-covalent)

K.1: 5 residues within 4Å: Chain A: G.52, N.262 Chain D: E.69, A.295, G.296 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: A:G.52, A:N.262, D:E.69, H2O.7, H2O.57 K.4: 5 residues within 4Å: Chain A: E.69, A.295, G.296 Chain D: G.52, N.262 5 PLIP interactions: 2 interactions with chain D, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: D:G.52, D:N.262, A:E.69, H2O.7, H2O.55 K.6: 5 residues within 4Å: Chain B: G.52, N.262 Chain C: E.69, A.295, G.296 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: B:G.52, B:N.262, C:E.69, H2O.23, H2O.39 K.10: 5 residues within 4Å: Chain B: E.69, A.295, G.296 Chain C: G.52, N.262 5 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: C:G.52, C:N.262, B:E.69, H2O.23, H2O.38

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

DMS.2: 6 residues within 4Å: Chain A: D.168, E.169, K.170, G.171, E.173, N.174 No protein-ligand interaction detected (PLIP) DMS.7: 2 residues within 4Å: Chain B: D.272, E.273 3 PLIP interactions: 3 interactions with chain B Water bridges: B:D.272, B:D.272 Salt bridges: B:D.272 DMS.8: 8 residues within 4Å: Chain A: M.65 Chain B: K.11, S.12, W.61 Chain C: M.65 Chain D: S.12, D.58, W.61 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B pi-Cation interactions: D:W.61, B:W.61 DMS.11: 2 residues within 4Å: Chain C: A.206, H.207 1 PLIP interactions: 1 interactions with chain C pi-Cation interactions: C:H.207 DMS.12: 5 residues within 4Å: Chain C: N.151, I.152, A.153, Q.228, P.339 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.228 Water bridges: C:F.154 DMS.13: 8 residues within 4Å: Chain A: K.11, S.12, D.58, W.61 Chain C: K.11, S.12, W.61 Chain D: M.65 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C pi-Cation interactions: A:W.61, C:W.61 DMS.16: 5 residues within 4Å: Chain D: Y.3, Y.324, D.327, K.328, A.331 No protein-ligand interaction detected (PLIP)

3 x PN9: (4Z)-4-({[(1E)-1-carboxy-3-(methylsulfanyl)propylidene]azaniumyl}methylidene)-2-methyl-5-[(phosphonooxy)methyl]-1,4-dihydropyridin-3-olate(Non-covalent)

PN9.3: 23 residues within 4Å: Chain A: F.36, T.49, 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, R.381, R.404, F.448, F.449 Chain D: Y.71 22 PLIP interactions: 21 interactions with chain A, 1 interactions with chain D 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:S.254, A:K.257 Water bridges: A:D.214, A:K.256, D:Y.71 Salt bridges: A:R.100, A:R.217, A:K.256, A:K.257, A:K.257, A:R.381, A:R.404 pi-Stacking: A:F.123 PN9.9: 23 residues within 4Å: Chain B: F.36, T.49, 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, R.381, R.404, F.448, F.449 Chain C: Y.71 20 PLIP interactions: 20 interactions with chain B 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:K.257 Water bridges: B:S.51, B:S.51 Salt bridges: B:R.100, B:R.217, B:K.256, B:K.257, B:K.257, B:R.381, B:R.404 pi-Stacking: B:F.123 PN9.14: 24 residues within 4Å: Chain B: Y.71 Chain C: 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, F.449 20 PLIP interactions: 19 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:T.49, C:Q.98, C:G.99, C:R.100, C:N.185, C:D.214, C:R.217, C:R.217, C:S.254, C:K.257 Water bridges: C:S.51, B:Y.291 Salt bridges: C:R.100, C:R.217, C:K.256, C:K.257, C:K.257, C:R.381, C:R.404 pi-Stacking: C:F.123

3 x CS: CESIUM ION(Non-functional Binders)

CS.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CS.15: 2 residues within 4Å: Chain C: Y.3, Y.324 No protein-ligand interaction detected (PLIP) CS.18: 2 residues within 4Å: Chain D: Y.3, Y.324 No protein-ligand interaction detected (PLIP)

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

PLP.17: 16 residues within 4Å: 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 17 PLIP interactions: 17 interactions with chain D Hydrophobic interactions: D:F.123, D:T.216, D:K.257 Hydrogen bonds: D:S.51, D:S.51, D:Q.98, D:G.99, D:R.100, D:N.185, D:R.217, D:R.217, D:K.257 Water bridges: D:K.256 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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