SMTL ID : 7fjk.1

Tyrosine phenol-lyase from pantoea agglomerans

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-tetramer

Ligands

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

PLP.1: 14 residues within 4Å: Chain A: S.51, Q.98, G.99, R.100, E.103, F.123, T.125, T.126, D.214, T.216, R.217, S.254, K.256, K.257 20 PLIP interactions: 19 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:F.123, A:T.216, A:K.257 Hydrogen bonds: A:S.51, A:Q.98, A:G.99, A:R.100, A:T.126, A:R.217, A:R.217, A:S.254, A:S.254, A:K.257 Water bridges: A:R.100, A:K.256, C:Y.71 Salt bridges: A:R.100, A:K.256, A:K.257 pi-Stacking: A:F.123 PLP.24: 14 residues within 4Å: Chain B: S.51, Q.98, G.99, R.100, E.103, F.123, T.125, T.126, D.214, T.216, R.217, S.254, K.256, K.257 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:T.216, B:K.257 Hydrogen bonds: B:S.51, B:Q.98, B:G.99, B:R.100, B:T.126, B:T.216, B:R.217, B:R.217, B:S.254, B:S.254 Salt bridges: B:R.100, B:K.257 pi-Stacking: B:F.123 PLP.32: 14 residues within 4Å: Chain C: S.51, Q.98, G.99, R.100, E.103, F.123, T.125, T.126, D.214, T.216, R.217, S.254, K.256, K.257 18 PLIP interactions: 17 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:F.123, C:T.216, C:K.257 Hydrogen bonds: C:S.51, C:S.51, C:Q.98, C:G.99, C:R.100, C:R.217, C:R.217, C:S.254 Water bridges: C:R.100, C:E.103, A:Y.71 Salt bridges: C:R.100, C:K.256, C:K.257 pi-Stacking: C:F.123 PLP.47: 14 residues within 4Å: Chain D: S.51, Q.98, G.99, R.100, E.103, F.123, T.125, T.126, D.214, T.216, R.217, S.254, K.256, K.257 17 PLIP interactions: 16 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:K.257 Hydrogen bonds: D:S.51, D:Q.98, D:G.99, D:R.100, D:T.216, D:R.217, D:R.217, D:S.254 Water bridges: D:R.100, D:E.103, D:K.256, B:Y.71 Salt bridges: D:R.100, D:K.256, D:K.257 pi-Stacking: D:F.123

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.2: 10 residues within 4Å: Chain A: K.11, S.12, D.58, W.61 Chain B: K.11, S.12, D.58, W.61 Chain C: M.65 Chain D: M.65 6 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D, 1 interactions with chain C, 2 interactions with chain B Hydrogen bonds: A:K.11, A:S.12, D:M.65, C:M.65, B:K.11, B:S.12

59 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 6 residues within 4Å: Chain A: M.18, I.19, R.24, Y.44, T.374, G.375 Ligand excluded by PLIP EDO.4: 6 residues within 4Å: Chain A: H.201, S.246, A.248, D.249, N.270 Ligands: EDO.19 Ligand excluded by PLIP EDO.5: 7 residues within 4Å: Chain A: S.365, S.369, M.372, I.434, R.435, L.437, F.455 Ligand excluded by PLIP EDO.6: 6 residues within 4Å: Chain A: E.14, T.15, S.40, K.41, I.43 Chain B: R.9 Ligand excluded by PLIP EDO.7: 4 residues within 4Å: Chain A: Y.3, Y.324, Y.414 Ligands: EDO.25 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain A: N.151, R.330, E.338, P.339 Ligands: EDO.14 Ligand excluded by PLIP EDO.9: 4 residues within 4Å: Chain A: P.335, I.336, E.338, R.351 Ligand excluded by PLIP EDO.10: 2 residues within 4Å: Chain A: E.86, K.238 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain A: N.185, L.186, F.346, R.381, R.404 Ligand excluded by PLIP EDO.12: 10 residues within 4Å: Chain A: E.14, T.53, N.54, A.55, N.262, V.411 Chain B: I.10, K.11 Chain C: E.69 Ligands: EDO.21 Ligand excluded by PLIP EDO.13: 3 residues within 4Å: Chain A: F.128, E.131, K.132 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain A: E.227, Q.228, R.323 Ligands: EDO.8 Ligand excluded by PLIP EDO.15: 3 residues within 4Å: Chain A: K.26, K.27, E.30 Ligand excluded by PLIP EDO.16: 4 residues within 4Å: Chain A: K.132 Chain C: Q.108, K.132, N.133 Ligand excluded by PLIP EDO.17: 3 residues within 4Å: Chain A: K.41 Chain C: E.75, Y.78 Ligand excluded by PLIP EDO.18: 3 residues within 4Å: Chain A: N.161, K.162, T.165 Ligand excluded by PLIP EDO.19: 8 residues within 4Å: Chain A: F.88, G.89, F.90, F.245, S.246, A.248, N.270 Ligands: EDO.4 Ligand excluded by PLIP EDO.20: 8 residues within 4Å: Chain A: A.62, G.63, I.66, E.300, I.304 Chain D: A.62 Ligands: EDO.22, EDO.65 Ligand excluded by PLIP EDO.21: 7 residues within 4Å: Chain A: E.14, T.53, V.411 Chain B: R.9 Chain C: E.69, A.70 Ligands: EDO.12 Ligand excluded by PLIP EDO.22: 6 residues within 4Å: Chain A: H.79, T.83, E.300, A.303, I.304 Ligands: EDO.20 Ligand excluded by PLIP EDO.25: 8 residues within 4Å: Chain A: Y.414, A.415 Chain B: Y.324, Y.414, A.415, D.418 Ligands: EDO.7, EDO.28 Ligand excluded by PLIP EDO.26: 6 residues within 4Å: Chain B: M.18, I.19, R.24, Y.44, T.374, G.375 Ligand excluded by PLIP EDO.27: 6 residues within 4Å: Chain B: A.72, G.73, F.77, Y.78, S.290 Chain D: F.449 Ligand excluded by PLIP EDO.28: 4 residues within 4Å: Chain B: Y.3, Y.324, Y.414 Ligands: EDO.25 Ligand excluded by PLIP EDO.29: 3 residues within 4Å: Chain B: L.109, M.274, A.277 Ligand excluded by PLIP EDO.30: 5 residues within 4Å: Chain B: Y.324, K.328, D.418, A.421, D.422 Ligand excluded by PLIP EDO.31: 6 residues within 4Å: Chain A: R.9 Chain B: E.14, T.53, V.411 Chain D: E.69, A.70 Ligand excluded by PLIP EDO.33: 6 residues within 4Å: Chain C: M.18, I.19, R.24, Y.44, T.374, G.375 Ligand excluded by PLIP EDO.34: 6 residues within 4Å: Chain C: M.1, P.4, A.5 Chain D: M.18, Y.44, V.419 Ligand excluded by PLIP EDO.35: 6 residues within 4Å: Chain A: F.449 Chain C: A.72, G.73, F.77, Y.78, S.290 Ligand excluded by PLIP EDO.36: 3 residues within 4Å: Chain C: I.336, E.338, R.351 Ligand excluded by PLIP EDO.37: 3 residues within 4Å: Chain C: E.227, Q.228, R.323 Ligand excluded by PLIP EDO.38: 6 residues within 4Å: Chain C: Y.3, Y.324, Y.414 Chain D: A.415, D.418 Ligands: EDO.40 Ligand excluded by PLIP EDO.39: 8 residues within 4Å: Chain B: M.65 Chain C: K.11, S.12, D.58, W.61 Chain D: S.12, W.61 Ligands: EDO.60 Ligand excluded by PLIP EDO.40: 7 residues within 4Å: Chain C: Y.414, A.415, D.418 Chain D: Y.414, A.415 Ligands: EDO.38, EDO.61 Ligand excluded by PLIP EDO.41: 6 residues within 4Å: Chain C: A.172, E.173, I.175, Y.207, G.208, I.209 Ligand excluded by PLIP EDO.42: 4 residues within 4Å: Chain C: L.109, E.273, M.274, A.277 Ligand excluded by PLIP EDO.43: 3 residues within 4Å: Chain C: K.226, E.233, Y.312 Ligand excluded by PLIP EDO.44: 5 residues within 4Å: Chain C: I.19, S.20, R.21, R.24, E.373 Ligand excluded by PLIP EDO.45: 6 residues within 4Å: Chain B: A.62 Chain C: A.62, G.63, I.66, E.300, I.304 Ligand excluded by PLIP EDO.46: 7 residues within 4Å: Chain C: F.88, G.89, F.90, F.245, S.246, A.248, N.270 Ligand excluded by PLIP EDO.48: 9 residues within 4Å: Chain B: E.69 Chain C: I.10, K.11 Chain D: E.14, T.53, N.54, A.55, V.411 Ligands: EDO.49 Ligand excluded by PLIP EDO.49: 7 residues within 4Å: Chain B: E.69, A.70 Chain C: R.9 Chain D: E.14, T.53, V.411 Ligands: EDO.48 Ligand excluded by PLIP EDO.50: 7 residues within 4Å: Chain C: R.9 Chain D: E.14, T.15, V.16, S.40, I.43 Ligands: EDO.52 Ligand excluded by PLIP EDO.51: 3 residues within 4Å: Chain D: R.21, V.25, M.372 Ligand excluded by PLIP EDO.52: 5 residues within 4Å: Chain D: T.15, V.16, S.17, K.41 Ligands: EDO.50 Ligand excluded by PLIP EDO.53: 6 residues within 4Å: Chain D: A.148, S.149, I.336, V.337, D.348, R.351 Ligand excluded by PLIP EDO.54: 4 residues within 4Å: Chain D: M.18, I.19, R.24, Y.44 Ligand excluded by PLIP EDO.55: 2 residues within 4Å: Chain D: Y.441, E.442 Ligand excluded by PLIP EDO.56: 2 residues within 4Å: Chain D: V.25, Q.29 Ligand excluded by PLIP EDO.57: 7 residues within 4Å: Chain D: A.145, H.146, A.148, K.155, A.187, V.337, E.338 Ligand excluded by PLIP EDO.58: 2 residues within 4Å: Chain A: Y.441, R.452 Ligand excluded by PLIP EDO.59: 6 residues within 4Å: Chain C: M.18, Y.44, V.419 Chain D: M.1, P.4, A.5 Ligand excluded by PLIP EDO.60: 8 residues within 4Å: Chain A: M.65 Chain C: S.12, W.61 Chain D: K.11, S.12, D.58, W.61 Ligands: EDO.39 Ligand excluded by PLIP EDO.61: 6 residues within 4Å: Chain C: A.415, D.418 Chain D: Y.3, Y.324, Y.414 Ligands: EDO.40 Ligand excluded by PLIP EDO.62: 7 residues within 4Å: Chain D: G.89, F.90, K.91, F.245, S.246, A.248, N.270 Ligand excluded by PLIP EDO.63: 6 residues within 4Å: Chain D: H.201, S.205, I.209, K.210, I.211, D.249 Ligand excluded by PLIP EDO.64: 5 residues within 4Å: Chain D: H.79, T.83, E.300, A.303, I.304 Ligand excluded by PLIP EDO.65: 6 residues within 4Å: Chain A: A.62 Chain D: A.62, G.63, I.66, E.300 Ligands: EDO.20 Ligand excluded by PLIP

1 x CIT: CITRIC ACID(Non-functional Binders)

CIT.23: 11 residues within 4Å: Chain A: R.100, F.123, T.124, T.125, M.379, R.381, R.404, F.448 Chain C: Y.71, V.283, M.288 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:R.100, A:T.124 Water bridges: A:R.100, A:R.381, A:R.404, A:R.404 Salt bridges: A:R.100, A:R.381, A:R.404

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Oikawa, D. et al., Faecal microbiota-dependent phenol production from tyrosine. To Be Published

Release Date

2022-08-10

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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