SMTL ID : 6t86.1 (1 other biounit)

Urocanate reductase in complex with FAD

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.56 Å

Oligo State

homo-tetramer

Ligands

4 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.1: 41 residues within 4Å: Chain A: I.10, G.11, S.12, G.13, G.14, A.15, I.33, E.34, K.35, M.36, G.40, G.41, N.42, S.43, I.45, S.46, G.47, A.48, E.49, T.155, K.156, A.157, A.191, T.192, G.193, T.216, G.217, H.218, D.224, M.228, H.392, H.393, G.421, E.422, R.432, G.435, N.436, A.437, Y.438, I.441 Ligands: SO4.8 32 PLIP interactions: 32 interactions with chain A Hydrogen bonds: A:S.12, A:S.12, A:G.13, A:G.14, A:A.15, A:K.35, A:K.35, A:N.42, A:N.42, A:S.43, A:S.43, A:S.46, A:S.46, A:G.47, A:E.49, A:E.49, A:A.157, A:A.157, A:H.218, A:H.393, A:E.422, A:R.432, A:R.432, A:G.435, A:A.437, A:Y.438 Water bridges: A:G.16, A:G.41, A:G.193, A:G.193, A:G.194 pi-Cation interactions: A:H.392 FAD.15: 41 residues within 4Å: Chain B: I.10, G.11, S.12, G.13, G.14, A.15, I.33, E.34, K.35, M.36, G.40, G.41, N.42, S.43, I.45, S.46, G.47, A.48, E.49, T.155, K.156, A.157, A.191, T.192, G.193, T.216, G.217, H.218, D.224, M.228, H.392, H.393, G.421, E.422, R.432, G.435, N.436, A.437, Y.438, I.441 Ligands: SO4.22 32 PLIP interactions: 32 interactions with chain B Hydrogen bonds: B:S.12, B:S.12, B:G.13, B:G.14, B:A.15, B:K.35, B:K.35, B:N.42, B:N.42, B:S.43, B:S.43, B:S.46, B:S.46, B:G.47, B:E.49, B:E.49, B:A.157, B:A.157, B:H.218, B:H.393, B:E.422, B:R.432, B:R.432, B:G.435, B:A.437, B:Y.438 Water bridges: B:G.16, B:G.41, B:G.193, B:G.193, B:G.194 pi-Cation interactions: B:H.392 FAD.29: 41 residues within 4Å: Chain C: I.10, G.11, S.12, G.13, G.14, A.15, I.33, E.34, K.35, M.36, G.40, G.41, N.42, S.43, I.45, S.46, G.47, A.48, E.49, T.155, K.156, A.157, A.191, T.192, G.193, T.216, G.217, H.218, D.224, M.228, H.392, H.393, G.421, E.422, R.432, G.435, N.436, A.437, Y.438, I.441 Ligands: SO4.36 38 PLIP interactions: 38 interactions with chain C Hydrogen bonds: C:S.12, C:S.12, C:G.13, C:G.14, C:A.15, C:K.35, C:K.35, C:N.42, C:N.42, C:S.43, C:S.43, C:S.46, C:S.46, C:G.47, C:E.49, C:E.49, C:A.157, C:A.157, C:H.218, C:D.224, C:H.393, C:E.422, C:E.422, C:R.432, C:R.432, C:G.435, C:A.437, C:Y.438 Water bridges: C:G.16, C:G.41, C:G.193, C:G.193, C:G.194, C:H.392, C:E.422, C:E.422, C:E.422 pi-Cation interactions: C:H.392 FAD.43: 41 residues within 4Å: Chain D: I.10, G.11, S.12, G.13, G.14, A.15, I.33, E.34, K.35, M.36, G.40, G.41, N.42, S.43, I.45, S.46, G.47, A.48, E.49, T.155, K.156, A.157, A.191, T.192, G.193, T.216, G.217, H.218, D.224, M.228, H.392, H.393, G.421, E.422, R.432, G.435, N.436, A.437, Y.438, I.441 Ligands: SO4.50 38 PLIP interactions: 38 interactions with chain D Hydrogen bonds: D:S.12, D:S.12, D:G.13, D:G.14, D:A.15, D:K.35, D:K.35, D:N.42, D:N.42, D:S.43, D:S.43, D:S.46, D:S.46, D:G.47, D:E.49, D:E.49, D:A.157, D:A.157, D:H.218, D:D.224, D:H.393, D:E.422, D:E.422, D:R.432, D:R.432, D:G.435, D:A.437, D:Y.438 Water bridges: D:G.16, D:G.41, D:G.193, D:G.193, D:G.194, D:H.392, D:E.422, D:E.422, D:E.422 pi-Cation interactions: D:H.392

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: Y.3, Y.5, P.150, H.152 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.5 GOL.3: 4 residues within 4Å: Chain A: H.152, T.153, H.175 Ligands: SO4.11 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.153, A:T.153, A:H.175 GOL.4: 3 residues within 4Å: Chain A: Y.245, L.257 Ligands: SO4.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.245 GOL.16: 4 residues within 4Å: Chain B: Y.3, Y.5, P.150, H.152 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.5 GOL.17: 4 residues within 4Å: Chain B: H.152, T.153, H.175 Ligands: SO4.25 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.153, B:T.153, B:H.175 GOL.18: 3 residues within 4Å: Chain B: Y.245, L.257 Ligands: SO4.22 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.245 GOL.30: 4 residues within 4Å: Chain C: Y.3, Y.5, P.150, H.152 No protein-ligand interaction detected (PLIP) GOL.31: 4 residues within 4Å: Chain C: H.152, T.153, H.175 Ligands: SO4.39 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Y.3, C:T.153, C:T.153, C:H.175 GOL.32: 3 residues within 4Å: Chain C: Y.245, L.257 Ligands: SO4.36 No protein-ligand interaction detected (PLIP) GOL.44: 4 residues within 4Å: Chain D: Y.3, Y.5, P.150, H.152 No protein-ligand interaction detected (PLIP) GOL.45: 4 residues within 4Å: Chain D: H.152, T.153, H.175 Ligands: SO4.53 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Y.3, D:T.153, D:T.153, D:H.175 GOL.46: 3 residues within 4Å: Chain D: Y.245, L.257 Ligands: SO4.50 No protein-ligand interaction detected (PLIP)

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

CL.5: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain A: K.237, N.238 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain A: E.22, W.100 Ligand excluded by PLIP CL.19: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.20: 2 residues within 4Å: Chain B: K.237, N.238 Ligand excluded by PLIP CL.21: 2 residues within 4Å: Chain B: E.22, W.100 Ligand excluded by PLIP CL.33: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.34: 2 residues within 4Å: Chain C: K.237, N.238 Ligand excluded by PLIP CL.35: 2 residues within 4Å: Chain C: E.22, W.100 Ligand excluded by PLIP CL.47: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.48: 2 residues within 4Å: Chain D: K.237, N.238 Ligand excluded by PLIP CL.49: 2 residues within 4Å: Chain D: E.22, W.100 Ligand excluded by PLIP

24 x SO4: SULFATE ION(Non-functional Binders)

SO4.8: 8 residues within 4Å: Chain A: F.117, R.283, H.392, R.432, G.434, G.435 Ligands: FAD.1, GOL.4 Ligand excluded by PLIP SO4.9: 2 residues within 4Å: Chain A: R.282, R.283 Ligand excluded by PLIP SO4.10: 5 residues within 4Å: Chain A: M.315, H.316, Q.317, G.318, E.319 Ligand excluded by PLIP SO4.11: 3 residues within 4Å: Chain A: N.154, H.175 Ligands: GOL.3 Ligand excluded by PLIP SO4.12: 2 residues within 4Å: Chain A: R.403, R.405 Ligand excluded by PLIP SO4.13: 3 residues within 4Å: Chain A: S.66, K.67, E.68 Ligand excluded by PLIP SO4.22: 8 residues within 4Å: Chain B: F.117, R.283, H.392, R.432, G.434, G.435 Ligands: FAD.15, GOL.18 Ligand excluded by PLIP SO4.23: 2 residues within 4Å: Chain B: R.282, R.283 Ligand excluded by PLIP SO4.24: 5 residues within 4Å: Chain B: M.315, H.316, Q.317, G.318, E.319 Ligand excluded by PLIP SO4.25: 3 residues within 4Å: Chain B: N.154, H.175 Ligands: GOL.17 Ligand excluded by PLIP SO4.26: 2 residues within 4Å: Chain B: R.403, R.405 Ligand excluded by PLIP SO4.27: 3 residues within 4Å: Chain B: S.66, K.67, E.68 Ligand excluded by PLIP SO4.36: 8 residues within 4Å: Chain C: F.117, R.283, H.392, R.432, G.434, G.435 Ligands: FAD.29, GOL.32 Ligand excluded by PLIP SO4.37: 2 residues within 4Å: Chain C: R.282, R.283 Ligand excluded by PLIP SO4.38: 5 residues within 4Å: Chain C: M.315, H.316, Q.317, G.318, E.319 Ligand excluded by PLIP SO4.39: 3 residues within 4Å: Chain C: N.154, H.175 Ligands: GOL.31 Ligand excluded by PLIP SO4.40: 2 residues within 4Å: Chain C: R.403, R.405 Ligand excluded by PLIP SO4.41: 3 residues within 4Å: Chain C: S.66, K.67, E.68 Ligand excluded by PLIP SO4.50: 8 residues within 4Å: Chain D: F.117, R.283, H.392, R.432, G.434, G.435 Ligands: FAD.43, GOL.46 Ligand excluded by PLIP SO4.51: 2 residues within 4Å: Chain D: R.282, R.283 Ligand excluded by PLIP SO4.52: 5 residues within 4Å: Chain D: M.315, H.316, Q.317, G.318, E.319 Ligand excluded by PLIP SO4.53: 3 residues within 4Å: Chain D: N.154, H.175 Ligands: GOL.45 Ligand excluded by PLIP SO4.54: 2 residues within 4Å: Chain D: R.403, R.405 Ligand excluded by PLIP SO4.55: 3 residues within 4Å: Chain D: S.66, K.67, E.68 Ligand excluded by PLIP

4 x NA: SODIUM ION(Non-functional Binders)

NA.14: 5 residues within 4Å: Chain A: T.394, M.395, G.396, E.422, T.424 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.395 NA.28: 5 residues within 4Å: Chain B: T.394, M.395, G.396, E.422, T.424 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.396 NA.42: 5 residues within 4Å: Chain C: T.394, M.395, G.396, E.422, T.424 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.424 Water bridges: C:T.424 NA.56: 5 residues within 4Å: Chain D: T.394, M.395, G.396, E.422, T.424 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:G.396 Water bridges: D:T.424

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Venskutonyte, R. et al., Structural characterization of the microbial enzyme urocanate reductase mediating imidazole propionate production. Nat Commun (2021)

Release Date

2021-03-03

Peptides

Urocanate reductase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Urocanate reductase

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