SMTL ID : 9ggj.1 (1 other biounit)

Crystal structure of argininosuccinate lyase from Arabidopsis thaliana (AtASL) in complex with biological substrate and products - argininosuccinate, argnine and fumarate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

2 x AS1: ARGININOSUCCINATE(Non-covalent)

AS1.1: 11 residues within 4Å: Chain A: S.27, R.113, N.114, V.117, Y.321, Q.326, K.329 Chain B: T.159, H.160 Chain D: K.287 Ligands: SO4.2 19 PLIP interactions: 11 interactions with chain A, 5 interactions with chain D, 3 interactions with chain B Hydrophobic interactions: A:R.113, A:V.117, A:V.117 Hydrogen bonds: A:S.27, A:N.114, A:N.114, A:Y.321, A:Q.326, D:N.289, B:T.159 Water bridges: A:D.31, A:R.323, D:T.279, D:G.280 Salt bridges: A:K.329, D:K.287, D:K.287, B:H.160, B:H.160 AS1.22: 13 residues within 4Å: Chain A: K.287, N.289 Chain C: T.159, H.160 Chain D: S.27, S.112, R.113, N.114, V.117, Y.321, Q.326, K.329 Ligands: SO4.24 21 PLIP interactions: 15 interactions with chain D, 4 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: D:V.117 Hydrogen bonds: D:S.27, D:R.113, D:R.113, D:N.114, D:N.114, D:N.114, D:Q.326, A:N.289 Water bridges: D:S.27, D:D.31, D:R.323, D:R.323, D:K.329, D:K.329, A:T.279 Salt bridges: D:K.329, A:K.287, A:K.287, C:H.160, C:H.160

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

SO4.2: 4 residues within 4Å: Chain A: H.108, S.112, R.113 Ligands: AS1.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.113 Salt bridges: A:H.108 SO4.3: 4 residues within 4Å: Chain A: S.281, S.282 Chain C: R.386, H.389 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:S.282, A:S.282 Salt bridges: C:R.386, C:H.389 SO4.4: 4 residues within 4Å: Chain A: N.356, E.357, D.358, R.359 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.356, A:E.357, A:D.358, A:R.359 Water bridges: A:R.359, A:R.359 Salt bridges: A:R.359 SO4.5: 4 residues within 4Å: Chain A: Q.407, G.430, V.431, E.432 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.407, A:V.431, A:E.432, A:E.432, A:N.433 Water bridges: A:E.432 SO4.6: 1 residues within 4Å: Chain A: K.416 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.416 SO4.10: 5 residues within 4Å: Chain B: H.108, S.112, R.113 Ligands: FUM.9, ARG.14 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Ligand interactions Hydrogen bonds: B:R.113 Salt bridges: B:H.108, R.14 SO4.11: 3 residues within 4Å: Chain B: S.281, S.282 Chain D: H.389 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain B Salt bridges: D:H.389 Hydrogen bonds: B:S.282, B:S.282 Water bridges: B:S.282 SO4.12: 4 residues within 4Å: Chain B: N.356, E.357, D.358, R.359 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.357, B:D.358, B:R.359 Salt bridges: B:R.359 SO4.13: 2 residues within 4Å: Chain B: T.56, D.57 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.57, B:D.57 Water bridges: B:D.57 SO4.15: 4 residues within 4Å: Chain C: H.108, S.112, R.113 Ligands: ARG.21 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.113 Salt bridges: C:H.108 SO4.16: 2 residues within 4Å: Chain C: T.56, D.57 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.57 Water bridges: C:T.56, C:S.58 SO4.17: 4 residues within 4Å: Chain A: H.389 Chain C: S.281, S.282, I.283 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:S.282, C:I.283 Salt bridges: A:H.389 SO4.24: 4 residues within 4Å: Chain D: H.108, S.112, R.113 Ligands: AS1.22 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:R.113 Water bridges: D:H.108, D:R.111 Salt bridges: D:H.108 SO4.25: 4 residues within 4Å: Chain D: N.356, E.357, D.358, R.359 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:D.358, D:R.359 Water bridges: D:E.357, D:E.357 Salt bridges: D:R.359

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

CL.7: 3 residues within 4Å: Chain A: Y.441 Chain B: I.211, R.213 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain A: I.211, R.213 Chain B: S.440, Y.441 Ligand excluded by PLIP CL.18: 4 residues within 4Å: Chain C: Y.441 Chain D: I.211, D.212, R.213 Ligand excluded by PLIP CL.19: 5 residues within 4Å: Chain C: I.211, D.212, R.213 Chain D: S.440, Y.441 Ligand excluded by PLIP CL.20: 1 residues within 4Å: Chain C: H.51 Ligand excluded by PLIP

1 x FUM: FUMARIC ACID(Non-covalent)

FUM.9: 10 residues within 4Å: Chain A: T.159, H.160, A.164, Q.165 Chain B: S.112, N.114, A.203 Chain C: K.287 Ligands: SO4.10, ARG.14 12 PLIP interactions: 4 interactions with chain B, 3 interactions with chain C, 3 interactions with chain A, 2 Ligand-Ligand interactions Hydrophobic interactions: B:A.203 Hydrogen bonds: B:S.112, B:S.112, B:N.114, A:T.159, A:Q.165 Water bridges: C:N.289, R.14 Salt bridges: C:K.287, C:K.287, A:H.160, R.14

2 x ARG: ARGININE(Non-covalent)

ARG.14: 9 residues within 4Å: Chain B: S.27, R.113, N.114, V.117, Y.321, Q.326, K.329 Ligands: FUM.9, SO4.10 10 PLIP interactions: 10 interactions with chain B, Hydrophobic interactions: B:R.113 Hydrogen bonds: B:S.27, B:N.114, B:Y.321, B:Q.326 Water bridges: B:D.31, B:D.31, B:D.87, B:K.329 Salt bridges: B:K.329 ARG.21: 8 residues within 4Å: Chain C: S.27, R.113, N.114, V.117, Y.321, Q.326, K.329 Ligands: SO4.15 20 PLIP interactions: 16 interactions with chain C, 4 Ligand-Ligand interactions Hydrophobic interactions: C:R.113, C:V.117 Hydrogen bonds: C:S.27, C:N.114, C:Y.321, C:Q.326 Water bridges: C:D.31, C:D.31, C:D.87, C:D.87, C:D.87, C:N.114, C:Y.321, C:Y.321, C:K.329, R.21, R.21, R.21, R.21 Salt bridges: C:K.329

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.23: 3 residues within 4Å: Chain D: R.82, R.85, D.98 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.82, D:R.82, D:R.85

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nielipinski, M. et al., Arabidopsis thaliana argininosuccinate lyase structure uncovers the role of serine as the catalytic base. J.Struct.Biol. (2024)

Release Date

2024-10-23

Peptides

Argininosuccinate lyase, chloroplastic: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Argininosuccinate lyase, chloroplastic

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