SMTL ID : 6rxa.1

EDDS lyase variant D290M/Y320M with bound formate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.44 Å

Oligo State

homo-tetramer

Ligands

12 x FMT: FORMIC ACID(Non-functional Binders)

FMT.1: 8 residues within 4Å: Chain A: S.280, S.281, I.282, M.283 Chain C: S.111, R.112, N.113 Ligands: FMT.2 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:S.280, A:S.281, A:S.281, A:I.282, C:R.112, C:R.112, C:N.113 FMT.2: 9 residues within 4Å: Chain A: S.280, M.283, K.286, N.288 Chain C: N.113, M.320 Chain D: T.158, Q.159 Ligands: FMT.1 6 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D, 3 interactions with chain A Hydrogen bonds: C:N.113, C:N.113, D:T.158, A:S.280, A:K.286, A:N.288 FMT.3: 7 residues within 4Å: Chain A: T.9, Y.26, G.278, T.279, M.290 Chain C: L.89, R.112 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:Y.26, A:Y.26, C:R.112, C:R.112 Water bridges: A:T.279 FMT.7: 8 residues within 4Å: Chain B: S.280, S.281, I.282, M.283 Chain D: S.111, R.112, N.113 Ligands: FMT.8 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain D Hydrogen bonds: B:S.280, B:S.281, B:S.281, B:I.282, D:R.112, D:R.112, D:N.113 FMT.8: 9 residues within 4Å: Chain B: S.280, M.283, K.286, N.288 Chain C: T.158, Q.159 Chain D: N.113, M.320 Ligands: FMT.7 6 PLIP interactions: 3 interactions with chain B, 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: B:S.280, B:K.286, B:N.288, D:N.113, D:N.113, C:T.158 FMT.9: 7 residues within 4Å: Chain B: T.9, Y.26, G.278, T.279, M.290 Chain D: L.89, R.112 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain B Hydrogen bonds: D:R.112, D:R.112, B:Y.26, B:Y.26 Water bridges: B:T.279 FMT.13: 8 residues within 4Å: Chain A: S.111, R.112, N.113 Chain C: S.280, S.281, I.282, M.283 Ligands: FMT.14 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain C Hydrogen bonds: A:R.112, A:R.112, A:N.113, C:S.280, C:S.281, C:S.281, C:I.282 FMT.14: 9 residues within 4Å: Chain A: N.113, M.320 Chain B: T.158, Q.159 Chain C: S.280, M.283, K.286, N.288 Ligands: FMT.13 6 PLIP interactions: 2 interactions with chain A, 3 interactions with chain C, 1 interactions with chain B Hydrogen bonds: A:N.113, A:N.113, C:S.280, C:K.286, C:N.288, B:T.158 FMT.15: 7 residues within 4Å: Chain A: L.89, R.112 Chain C: T.9, Y.26, G.278, T.279, M.290 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:Y.26, C:Y.26, A:R.112, A:R.112 Water bridges: C:T.279 FMT.19: 8 residues within 4Å: Chain B: S.111, R.112, N.113 Chain D: S.280, S.281, I.282, M.283 Ligands: FMT.20 7 PLIP interactions: 4 interactions with chain D, 3 interactions with chain B Hydrogen bonds: D:S.280, D:S.281, D:S.281, D:I.282, B:R.112, B:R.112, B:N.113 FMT.20: 9 residues within 4Å: Chain A: T.158, Q.159 Chain B: N.113, M.320 Chain D: S.280, M.283, K.286, N.288 Ligands: FMT.19 6 PLIP interactions: 3 interactions with chain D, 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: D:S.280, D:K.286, D:N.288, A:T.158, B:N.113, B:N.113 FMT.21: 7 residues within 4Å: Chain B: L.89, R.112 Chain D: T.9, Y.26, G.278, T.279, M.290 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:Y.26, D:Y.26, B:R.112, B:R.112 Water bridges: D:T.279

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: D.151, T.152, V.153, R.357, W.437 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.151 Water bridges: A:R.357 GOL.10: 5 residues within 4Å: Chain B: D.151, T.152, V.153, R.357, W.437 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.151 Water bridges: B:R.357 GOL.16: 5 residues within 4Å: Chain C: D.151, T.152, V.153, R.357, W.437 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.151 Water bridges: C:R.357 GOL.22: 5 residues within 4Å: Chain D: D.151, T.152, V.153, R.357, W.437 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.151 Water bridges: D:R.357

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

NA.5: 9 residues within 4Å: Chain A: R.185, E.188, R.192, E.240 Chain B: R.185, E.188, R.192, E.240 Ligands: NA.11 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.188, A:E.188, A:R.192, B:R.192 NA.6: 5 residues within 4Å: Chain A: K.181, R.185 Chain B: R.192, D.236, H.237 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:K.181, A:R.185, B:H.237 Water bridges: B:R.192 NA.11: 9 residues within 4Å: Chain A: R.185, E.188, R.192, E.240 Chain B: R.185, E.188, R.192, E.240 Ligands: NA.5 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:E.188, A:R.192, B:E.188, B:R.192 NA.12: 5 residues within 4Å: Chain A: R.192, D.236, H.237 Chain B: K.181, R.185 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:H.237, B:K.181, B:R.185 NA.17: 9 residues within 4Å: Chain C: R.185, E.188, R.192, E.240 Chain D: R.185, E.188, R.192, E.240 Ligands: NA.23 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:E.188, D:R.192, D:E.240, C:R.192 NA.18: 5 residues within 4Å: Chain C: K.181, R.185 Chain D: R.192, D.236, H.237 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:H.237, C:K.181, C:R.185 NA.23: 9 residues within 4Å: Chain C: R.185, E.188, R.192, E.240 Chain D: R.185, E.188, R.192, E.240 Ligands: NA.17 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:E.188, D:R.192, C:R.192, C:E.240 NA.24: 5 residues within 4Å: Chain C: R.192, D.236, H.237 Chain D: K.181, R.185 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:K.181, D:R.185, C:H.237

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, J. et al., Engineered C-N Lyase: Enantioselective Synthesis of Chiral Synthons for Artificial Dipeptide Sweeteners. Angew.Chem.Int.Ed.Engl. (2020)

Release Date

2019-10-30

Peptides

Argininosuccinate lyase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Argininosuccinate lyase

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