SMTL ID : 6t88.1

Urocanate reductase in complex with imidazole propionate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-dimer

Ligands

16 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 6 residues within 4Å: Chain A: L.21, E.22, A.25, W.100, Y.104, R.446 Ligand excluded by PLIP GOL.2: 4 residues within 4Å: Chain A: Y.110, P.111, D.112, Q.113 Ligand excluded by PLIP GOL.3: 5 residues within 4Å: Chain A: E.314, M.315, H.316, Q.317, G.318 Ligand excluded by PLIP GOL.4: 7 residues within 4Å: Chain A: P.250, T.251, D.326, G.327, L.328, F.342, K.386 Ligand excluded by PLIP GOL.5: 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.6: 9 residues within 4Å: Chain A: T.64, D.65, L.69, S.121, V.122 Chain B: K.364, D.365, E.366, N.369 Ligand excluded by PLIP GOL.13: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP GOL.14: 12 residues within 4Å: Chain A: Q.116, F.117, G.118, R.262, F.263, L.280, E.281, R.282, R.283, I.286, R.371 Ligands: CL.12 Ligand excluded by PLIP GOL.15: 6 residues within 4Å: Chain B: L.21, E.22, A.25, W.100, Y.104, R.446 Ligand excluded by PLIP GOL.16: 4 residues within 4Å: Chain B: Y.110, P.111, D.112, Q.113 Ligand excluded by PLIP GOL.17: 5 residues within 4Å: Chain B: E.314, M.315, H.316, Q.317, G.318 Ligand excluded by PLIP GOL.18: 7 residues within 4Å: Chain B: P.250, T.251, D.326, G.327, L.328, F.342, K.386 Ligand excluded by PLIP GOL.19: 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.20: 9 residues within 4Å: Chain A: K.364, D.365, E.366, N.369 Chain B: T.64, D.65, L.69, S.121, V.122 Ligand excluded by PLIP GOL.27: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP GOL.28: 12 residues within 4Å: Chain B: Q.116, F.117, G.118, R.262, F.263, L.280, E.281, R.282, R.283, I.286, R.371 Ligands: CL.26 Ligand excluded by PLIP

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

FAD.7: 47 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, M.228, 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: MWQ.8 36 PLIP interactions: 36 interactions with chain A Hydrophobic interactions: A:N.42, A:I.255 Hydrogen bonds: A:S.12, A:G.13, A:G.14, A:A.15, A:E.34, A:E.34, A:K.35, A:K.35, A:N.42, A:N.42, A:N.42, A:N.42, 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:A.157, A:G.193, A:H.393, A:E.422, 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.194, A:V.423 FAD.21: 47 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, M.228, 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: MWQ.22 39 PLIP interactions: 39 interactions with chain B Hydrophobic interactions: B:N.42, B:I.255 Hydrogen bonds: B:S.12, B:G.13, B:G.14, B:A.15, B:E.34, B:E.34, B:K.35, B:K.35, B:N.42, B:N.42, B:N.42, B:N.42, 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:A.157, B:G.193, B:D.224, B:H.393, B:E.422, B:E.422, 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.194, B:V.423

2 x MWQ: 3-(1~{H}-imidazol-5-yl)propanoic acid(Non-covalent)

MWQ.8: 14 residues within 4Å: Chain A: G.47, E.49, F.115, F.117, Y.245, I.255, L.257, D.260, F.263, H.392, R.432, G.434, G.435 Ligands: FAD.7 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.117, A:Y.245 Hydrogen bonds: A:E.49, A:G.435 Water bridges: A:H.392 Salt bridges: A:H.392, A:R.432 pi-Stacking: A:F.117 MWQ.22: 14 residues within 4Å: Chain B: G.47, E.49, F.115, F.117, Y.245, I.255, L.257, D.260, F.263, H.392, R.432, G.434, G.435 Ligands: FAD.21 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.117, B:Y.245 Hydrogen bonds: B:E.49, B:G.435 Water bridges: B:H.392 Salt bridges: B:H.392, B:R.432 pi-Stacking: B:F.117

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

NA.9: 6 residues within 4Å: Chain A: T.394, M.395, G.396, E.422, T.424, G.425 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.394 Water bridges: A:T.424 NA.23: 6 residues within 4Å: Chain B: T.394, M.395, G.396, E.422, T.424, G.425 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:M.395 Water bridges: B:T.424

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

CL.10: 4 residues within 4Å: Chain A: M.61, Q.113, L.114, K.123 Ligand excluded by PLIP CL.11: 5 residues within 4Å: Chain A: G.118, R.282, R.283, N.431, L.433 Ligand excluded by PLIP CL.12: 5 residues within 4Å: Chain A: F.117, G.118, R.283, G.434 Ligands: GOL.14 Ligand excluded by PLIP CL.24: 4 residues within 4Å: Chain B: M.61, Q.113, L.114, K.123 Ligand excluded by PLIP CL.25: 5 residues within 4Å: Chain B: G.118, R.282, R.283, N.431, L.433 Ligand excluded by PLIP CL.26: 5 residues within 4Å: Chain B: F.117, G.118, R.283, G.434 Ligands: GOL.28 Ligand excluded by PLIP

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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