SMTL ID : 6t87.1

Urocanate reductase in complex with urocanate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.56 Å

Oligo State

homo-dimer

Ligands

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

FAD.1: 46 residues within 4Å: Chain A: I.10, G.11, S.12, G.13, G.14, A.15, G.16, 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, F.117, T.155, K.156, A.157, A.191, T.192, G.193, T.216, G.217, H.218, G.220, D.224, I.255, L.257, H.392, H.393, G.421, E.422, V.423, R.432, G.435, N.436, A.437, Y.438, I.441 Ligands: URO.2 30 PLIP interactions: 30 interactions with chain A Hydrophobic interactions: A:I.255 Hydrogen bonds: A:S.12, A:G.13, A:A.15, A:K.35, A:K.35, A:N.42, A:N.42, A:S.43, A:S.43, A:S.43, A:S.46, A:G.47, A:A.48, A:E.49, A:E.49, A:A.157, A:G.193, A:D.224, A:E.422, A:E.422, A:R.432, A:G.435, A:A.437, A:Y.438 Water bridges: A:G.16, A:E.34, A:G.41, A:G.194, A:V.423 FAD.18: 46 residues within 4Å: Chain B: I.10, G.11, S.12, G.13, G.14, A.15, G.16, 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, F.117, T.155, K.156, A.157, A.191, T.192, G.193, T.216, G.217, H.218, G.220, D.224, I.255, L.257, H.392, H.393, G.421, E.422, V.423, R.432, G.435, N.436, A.437, Y.438, I.441 Ligands: URO.19 33 PLIP interactions: 33 interactions with chain B Hydrophobic interactions: B:I.255 Hydrogen bonds: B:S.12, B:G.13, B:A.15, B:K.35, B:K.35, B:N.42, B:N.42, B:S.43, B:S.43, B:S.43, B:S.46, B:G.47, B:A.48, B:E.49, B:E.49, B:E.49, B:A.157, B:G.193, B:D.224, B:D.224, B:E.422, B:E.422, B:E.422, B:R.432, B:G.435, B:A.437, B:Y.438 Water bridges: B:G.16, B:E.34, B:G.41, B:G.194, B:V.423

2 x URO: (2E)-3-(1H-IMIDAZOL-4-YL)ACRYLIC ACID(Non-covalent)

URO.2: 14 residues within 4Å: Chain A: G.47, E.49, F.117, Y.245, I.255, L.257, D.260, R.283, H.392, R.432, G.434, G.435 Ligands: FAD.1, GOL.9 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.117, A:Y.245 Hydrogen bonds: A:D.260, A:G.435 Water bridges: A:Y.245 Salt bridges: A:R.283, A:H.392, A:R.432 URO.19: 14 residues within 4Å: Chain B: G.47, E.49, F.117, Y.245, I.255, L.257, D.260, R.283, H.392, R.432, G.434, G.435 Ligands: FAD.18, GOL.26 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:F.117, B:Y.245 Hydrogen bonds: B:D.260, B:G.435 Water bridges: B:Y.245, B:D.260 Salt bridges: B:R.283, B:H.392, B:R.432

16 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: I.38, L.44, I.45 Ligand excluded by PLIP GOL.4: 5 residues within 4Å: Chain A: E.314, M.315, H.316, Q.317, G.318 Ligand excluded by PLIP GOL.5: 6 residues within 4Å: Chain A: P.250, D.326, G.327, L.328, F.342, K.386 Ligand excluded by PLIP GOL.6: 3 residues within 4Å: Chain A: D.163, Q.164, T.165 Ligand excluded by PLIP GOL.7: 5 residues within 4Å: Chain A: E.22, A.25, W.100, Y.104, R.446 Ligand excluded by PLIP GOL.8: 7 residues within 4Å: Chain A: I.71, S.72, L.75, F.80 Chain B: F.276, Q.293, F.368 Ligand excluded by PLIP GOL.9: 9 residues within 4Å: Chain A: E.49, F.115, F.117, I.127, H.131, D.260, F.263, F.264 Ligands: URO.2 Ligand excluded by PLIP GOL.10: 4 residues within 4Å: Chain A: Y.110, P.111, D.112, Q.113 Ligand excluded by PLIP GOL.20: 3 residues within 4Å: Chain B: I.38, L.44, I.45 Ligand excluded by PLIP GOL.21: 5 residues within 4Å: Chain B: E.314, M.315, H.316, Q.317, G.318 Ligand excluded by PLIP GOL.22: 6 residues within 4Å: Chain B: P.250, D.326, G.327, L.328, F.342, K.386 Ligand excluded by PLIP GOL.23: 3 residues within 4Å: Chain B: D.163, Q.164, T.165 Ligand excluded by PLIP GOL.24: 5 residues within 4Å: Chain B: E.22, A.25, W.100, Y.104, R.446 Ligand excluded by PLIP GOL.25: 7 residues within 4Å: Chain A: F.276, Q.293, F.368 Chain B: I.71, S.72, L.75, F.80 Ligand excluded by PLIP GOL.26: 9 residues within 4Å: Chain B: E.49, F.115, F.117, I.127, H.131, D.260, F.263, F.264 Ligands: URO.19 Ligand excluded by PLIP GOL.27: 4 residues within 4Å: Chain B: Y.110, P.111, D.112, Q.113 Ligand excluded by PLIP

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

SO4.11: 7 residues within 4Å: Chain A: F.115, F.117, G.118, Y.245, R.262, F.263, R.283 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.118, A:R.283 Water bridges: A:Y.245, A:R.262, A:R.262, A:R.282 Salt bridges: A:R.262, A:R.283 SO4.12: 2 residues within 4Å: Chain A: R.403, R.405 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.405 Salt bridges: A:R.403 SO4.13: 2 residues within 4Å: Chain A: H.175, N.176 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.176 Salt bridges: A:H.175 SO4.14: 3 residues within 4Å: Chain A: K.354, N.357, S.378 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.357 Water bridges: A:K.354, A:K.354 Salt bridges: A:K.354 SO4.28: 7 residues within 4Å: Chain B: F.115, F.117, G.118, Y.245, R.262, F.263, R.283 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:G.118, B:R.283 Water bridges: B:Y.245, B:R.262, B:R.262, B:E.281, B:R.282 Salt bridges: B:R.262, B:R.283 SO4.29: 2 residues within 4Å: Chain B: R.403, R.405 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.405 Salt bridges: B:R.403 SO4.30: 2 residues within 4Å: Chain B: H.175, N.176 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.176 Salt bridges: B:H.175 SO4.31: 3 residues within 4Å: Chain B: K.354, N.357, S.378 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.357 Water bridges: B:K.354, B:K.354 Salt bridges: B:K.354

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

CL.15: 2 residues within 4Å: Chain A: K.237, N.238 Ligand excluded by PLIP CL.16: 2 residues within 4Å: Chain A: S.66, K.67 Ligand excluded by PLIP CL.32: 2 residues within 4Å: Chain B: K.237, N.238 Ligand excluded by PLIP CL.33: 2 residues within 4Å: Chain B: S.66, K.67 Ligand excluded by PLIP

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

NA.17: 6 residues within 4Å: Chain A: T.394, M.395, G.396, E.422, T.424, G.425 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.394 Water bridges: A:T.394, A:T.424 NA.34: 6 residues within 4Å: Chain B: T.394, M.395, G.396, E.422, T.424, G.425 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.396 Water bridges: B:T.394, B: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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Urocanate reductase

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