SMTL ID : 6rx8.1

EDDS lyase variant D290M/Y320M with bound fumarate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.92 Å

Oligo State

homo-tetramer

Ligands

8 x FUM: FUMARIC ACID(Non-covalent)

FUM.1: 12 residues within 4Å: Chain A: S.280, S.281, I.282, M.283, K.286, N.288 Chain B: H.107, S.111, R.112, N.113 Chain C: T.158, Q.159 15 PLIP interactions: 9 interactions with chain A, 4 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: A:I.282 Hydrogen bonds: A:S.280, A:S.280, A:S.281, A:S.281, A:I.282, A:N.288, B:R.112, B:N.113, C:T.158, C:Q.159 Water bridges: A:T.279, B:R.112 Salt bridges: A:K.286, B:R.112 FUM.2: 6 residues within 4Å: Chain A: Y.26, G.278, M.290, R.294 Chain B: R.112, M.320 8 PLIP interactions: 3 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:Y.26 Water bridges: A:T.279, B:R.112, B:R.112, B:R.112 Salt bridges: A:R.294, B:R.112, B:R.112 FUM.5: 12 residues within 4Å: Chain A: H.107, S.111, R.112, N.113 Chain B: S.280, S.281, I.282, M.283, K.286, N.288 Chain D: T.158, Q.159 15 PLIP interactions: 4 interactions with chain A, 9 interactions with chain B, 2 interactions with chain D Hydrogen bonds: A:R.112, A:N.113, B:S.280, B:S.280, B:S.281, B:S.281, B:I.282, B:N.288, D:T.158, D:Q.159 Water bridges: A:R.112, B:T.279 Salt bridges: A:R.112, B:K.286 Hydrophobic interactions: B:I.282 FUM.6: 6 residues within 4Å: Chain A: R.112, M.320 Chain B: Y.26, G.278, M.290, R.294 8 PLIP interactions: 3 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:Y.26 Water bridges: B:T.279, A:R.112, A:R.112, A:R.112 Salt bridges: B:R.294, A:R.112, A:R.112 FUM.9: 12 residues within 4Å: Chain A: T.158, Q.159 Chain C: S.280, S.281, I.282, M.283, K.286, N.288 Chain D: H.107, S.111, R.112, N.113 15 PLIP interactions: 9 interactions with chain C, 4 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: C:I.282 Hydrogen bonds: C:S.280, C:S.280, C:S.281, C:S.281, C:I.282, C:N.288, D:R.112, D:N.113, A:T.158, A:Q.159 Water bridges: C:T.279, D:R.112 Salt bridges: C:K.286, D:R.112 FUM.10: 6 residues within 4Å: Chain C: Y.26, G.278, M.290, R.294 Chain D: R.112, M.320 8 PLIP interactions: 3 interactions with chain C, 5 interactions with chain D Hydrogen bonds: C:Y.26 Water bridges: C:T.279, D:R.112, D:R.112, D:R.112 Salt bridges: C:R.294, D:R.112, D:R.112 FUM.13: 12 residues within 4Å: Chain B: T.158, Q.159 Chain C: H.107, S.111, R.112, N.113 Chain D: S.280, S.281, I.282, M.283, K.286, N.288 15 PLIP interactions: 9 interactions with chain D, 2 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: D:I.282 Hydrogen bonds: D:S.280, D:S.280, D:S.281, D:S.281, D:I.282, D:N.288, B:T.158, B:Q.159, C:R.112, C:N.113 Water bridges: D:T.279, C:R.112 Salt bridges: D:K.286, C:R.112 FUM.14: 6 residues within 4Å: Chain C: R.112, M.320 Chain D: Y.26, G.278, M.290, R.294 8 PLIP interactions: 3 interactions with chain D, 5 interactions with chain C Hydrogen bonds: D:Y.26 Water bridges: D:T.279, C:R.112, C:R.112, C:R.112 Salt bridges: D:R.294, C:R.112, C:R.112

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

NA.3: 9 residues within 4Å: Chain A: R.185, E.188, R.192, E.240 Chain D: R.185, E.188, R.192, E.240 Ligands: NA.15 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:R.192, D:E.240, D:E.240, A:E.188, A:R.192 NA.4: 5 residues within 4Å: Chain A: K.181, R.185 Chain D: R.192, D.236, H.237 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:H.237, A:K.181, A:R.185 Water bridges: D:D.236, D:D.236, D:D.236, D:H.237 NA.7: 9 residues within 4Å: Chain B: R.185, E.188, R.192, E.240 Chain C: R.185, E.188, R.192, E.240 Ligands: NA.11 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:R.192, C:E.240, B:E.188, B:E.188, B:R.192 NA.8: 5 residues within 4Å: Chain B: K.181, R.185 Chain C: R.192, D.236, H.237 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:H.237, B:K.181, B:R.185 Water bridges: C:D.236, C:D.236, C:D.236, C:H.237 NA.11: 9 residues within 4Å: Chain B: R.185, E.188, R.192, E.240 Chain C: R.185, E.188, R.192, E.240 Ligands: NA.7 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:E.188, C:R.192, C:E.240, B:E.188, B:R.192 NA.12: 5 residues within 4Å: Chain B: R.192, D.236, H.237 Chain C: K.181, R.185 7 PLIP interactions: 2 interactions with chain C, 5 interactions with chain B Hydrogen bonds: C:K.181, C:R.185, B:H.237 Water bridges: B:D.236, B:D.236, B:D.236, B:H.237 NA.15: 9 residues within 4Å: Chain A: R.185, E.188, R.192, E.240 Chain D: R.185, E.188, R.192, E.240 Ligands: NA.3 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:R.192, D:E.240, D:E.240, A:E.188, A:R.192 NA.16: 5 residues within 4Å: Chain A: R.192, D.236, H.237 Chain D: K.181, R.185 7 PLIP interactions: 2 interactions with chain D, 5 interactions with chain A Hydrogen bonds: D:K.181, D:R.185, A:H.237 Water bridges: A:D.236, A:D.236, A:D.236, A: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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