SMTL ID : 9ggj.2 (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

3 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: SO4.4 23 PLIP interactions: 16 interactions with chain A, 5 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: A:V.117 Hydrogen bonds: A:S.27, A:R.113, A:N.114, A:N.114, A:Y.321, A:Q.326, D:N.289 Water bridges: A:D.31, A:D.31, A:D.31, A:D.87, A:R.113, A:Y.321, A:R.323, A:K.329, D:K.287, D:D.291 Salt bridges: A:K.329, D:K.287, D:K.287, B:H.160, B:H.160 AS1.13: 13 residues within 4Å: Chain B: N.289 Chain C: S.27, S.112, R.113, N.114, V.117, A.203, Y.321, Q.326, K.329 Chain D: T.159, H.160 Ligands: SO4.16 20 PLIP interactions: 15 interactions with chain C, 2 interactions with chain B, 3 interactions with chain D Hydrophobic interactions: C:R.113 Hydrogen bonds: C:S.27, C:R.113, C:R.113, C:N.114, C:N.114, C:N.114, C:Y.321, C:Q.326, B:N.289, D:T.159 Water bridges: C:S.27, C:D.31, C:R.323, C:R.323, C:K.329 Salt bridges: C:K.329, B:K.287, D:H.160, D:H.160 AS1.18: 11 residues within 4Å: Chain A: K.287, N.289 Chain C: T.159, H.160 Chain D: S.27, R.113, N.114, Y.321, Q.326, K.329 Ligands: SO4.19 19 PLIP interactions: 12 interactions with chain D, 3 interactions with chain C, 4 interactions with chain A Hydrogen bonds: D:S.27, D:N.114, D:N.114, D:N.114, D:Y.321, D:Q.326, C:T.159, A:N.289 Water bridges: D:D.31, D:D.31, D:D.87, D:R.236, D:K.329, A:T.279 Salt bridges: D:K.329, C:H.160, C:H.160, A:K.287, A:K.287

1 x FUM: FUMARIC ACID(Non-covalent)

FUM.2: 8 residues within 4Å: Chain A: T.159, H.160, A.164, Q.165 Chain B: N.114, A.203 Ligands: SO4.11, ARG.12 8 PLIP interactions: 3 interactions with chain A, 2 interactions with chain C, 2 interactions with chain B, 1 Ligand-Ligand interactions Hydrogen bonds: A:T.159, A:Q.165, B:N.114 Salt bridges: A:H.160, C:K.287, C:K.287, R.12 Hydrophobic interactions: B:A.203

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

SO4.3: 4 residues within 4Å: Chain A: S.281, S.282, I.283 Chain C: H.389 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:S.282, A:I.283 Salt bridges: C:H.389 SO4.4: 4 residues within 4Å: Chain A: H.108, S.112, R.113 Ligands: AS1.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.113 Water bridges: A:R.113, A:R.113, A:R.113 Salt bridges: A:H.108, A:R.113 SO4.5: 4 residues within 4Å: Chain A: N.356, E.357, D.358, R.359 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.357, A:D.358, A:R.359 Salt bridges: A:R.359 SO4.6: 3 residues within 4Å: Chain A: T.56, D.57, S.58 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.57, A:S.58 SO4.8: 4 residues within 4Å: Chain B: S.281, S.282 Chain D: R.386, H.389 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:S.281, B:S.282 Salt bridges: D:R.386, D:H.389 SO4.9: 4 residues within 4Å: Chain B: N.356, E.357, D.358, R.359 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:D.358, B:D.358, B:R.359 Water bridges: B:E.357, B:E.357, B:E.357 Salt bridges: B:R.359 SO4.10: 3 residues within 4Å: Chain B: I.55, T.56, D.57 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.57, B:D.57, B:D.57 SO4.11: 5 residues within 4Å: Chain B: H.108, S.112, R.113 Ligands: FUM.2, ARG.12 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Ligand interactions Hydrogen bonds: B:R.113 Water bridges: B:R.113, R.12 Salt bridges: B:H.108, R.12 SO4.16: 4 residues within 4Å: Chain C: H.108, S.112, R.113 Ligands: AS1.13 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.113 Water bridges: C:S.112, C:R.113 Salt bridges: C:H.108, C:R.113 SO4.19: 5 residues within 4Å: Chain D: H.108, R.111, S.112, R.113 Ligands: AS1.18 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.112, D:R.113 Salt bridges: D:H.108 SO4.20: 4 residues within 4Å: Chain D: N.356, E.357, D.358, R.359 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:N.356, D:E.357, D:D.358, D:R.359 Water bridges: D:T.272, D:R.359, D:R.359 Salt bridges: D:R.359 SO4.21: 2 residues within 4Å: Chain D: T.56, D.57 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:D.57 Water bridges: D:T.56, D:S.58, D:S.58 SO4.22: 4 residues within 4Å: Chain C: K.105, H.108 Chain D: F.385, R.386 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain C Water bridges: D:R.386, C:H.108, C:H.108 Salt bridges: D:R.386, C:H.108

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

CL.7: 3 residues within 4Å: Chain A: I.211, R.213 Chain B: Y.441 Ligand excluded by PLIP CL.17: 5 residues within 4Å: Chain C: S.440, Y.441 Chain D: I.211, D.212, R.213 Ligand excluded by PLIP

1 x ARG: ARGININE(Non-covalent)

ARG.12: 10 residues within 4Å: Chain B: S.27, R.113, N.114, V.117, Y.321, F.325, Q.326, K.329 Ligands: FUM.2, SO4.11 13 PLIP interactions: 11 interactions with chain B, 2 Ligand-Ligand interactions Hydrophobic interactions: B:R.113, B:V.117 Hydrogen bonds: B:S.27, B:N.114, B:N.114, B:Q.326, R.12, R.12 Water bridges: B:R.113, B:R.323, B:K.329, B:K.329 Salt bridges: B:K.329

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.14: 3 residues within 4Å: Chain C: T.56, D.57, S.58 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.57, C:S.58 Water bridges: C:D.57 GOL.15: 2 residues within 4Å: Chain C: H.51, M.215 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:H.51 Water bridges: C:M.215, C:N.218, C:N.218

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
E

B
F

C
G

D
H

Argininosuccinate lyase, chloroplastic

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