SMTL ID : 9ggi.2 (1 other biounit)

Crystal structure of argininosuccinate lyase from Arabidopsis thaliana (AtASL)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-tetramer

Ligands

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

CL.1: 3 residues within 4Å: Chain A: Y.441 Chain B: I.211, R.213 Ligand excluded by PLIP CL.2: 4 residues within 4Å: Chain A: I.211, R.213 Chain B: S.440, Y.441 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

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

SO4.3: 4 residues within 4Å: Chain A: N.356, E.357, D.358, R.359 Ligand excluded by PLIP SO4.4: 5 residues within 4Å: Chain A: K.361, Q.407, G.430, V.431, E.432 Ligand excluded by PLIP SO4.5: 3 residues within 4Å: Chain A: K.380, F.428, K.437 Ligand excluded by PLIP SO4.9: 4 residues within 4Å: Chain B: N.356, E.357, D.358, R.359 Ligand excluded by PLIP SO4.10: 4 residues within 4Å: Chain B: S.281, S.282, I.283 Chain D: H.389 Ligand excluded by PLIP SO4.11: 2 residues within 4Å: Chain B: T.56, D.57 Ligand excluded by PLIP SO4.12: 1 residues within 4Å: Chain B: Q.52 Ligand excluded by PLIP SO4.13: 5 residues within 4Å: Chain A: N.114, A.203 Chain B: T.159 Chain D: K.287 Ligands: GOL.8 Ligand excluded by PLIP SO4.14: 4 residues within 4Å: Chain B: Q.407, G.430, V.431, E.432 Ligand excluded by PLIP SO4.15: 3 residues within 4Å: Chain B: K.380, F.428, K.437 Ligand excluded by PLIP SO4.20: 5 residues within 4Å: Chain A: S.281, S.282, I.283 Chain C: R.386, H.389 Ligand excluded by PLIP SO4.21: 4 residues within 4Å: Chain A: H.389 Chain C: S.281, S.282, I.283 Ligand excluded by PLIP SO4.22: 4 residues within 4Å: Chain C: H.108, S.112, R.113 Ligands: SO4.31 Ligand excluded by PLIP SO4.23: 2 residues within 4Å: Chain C: T.56, D.57 Ligand excluded by PLIP SO4.24: 6 residues within 4Å: Chain A: K.287, N.289 Chain C: T.159, H.160 Chain D: N.114 Ligands: GOL.32 Ligand excluded by PLIP SO4.25: 4 residues within 4Å: Chain C: Q.407, G.430, V.431, E.432 Ligand excluded by PLIP SO4.28: 3 residues within 4Å: Chain B: H.389 Chain D: S.281, S.282 Ligand excluded by PLIP SO4.29: 4 residues within 4Å: Chain D: N.356, E.357, D.358, R.359 Ligand excluded by PLIP SO4.30: 2 residues within 4Å: Chain D: T.56, D.57 Ligand excluded by PLIP SO4.31: 6 residues within 4Å: Chain B: K.287 Chain C: N.114, A.203 Chain D: T.159, H.160 Ligands: SO4.22 Ligand excluded by PLIP

11 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 5 residues within 4Å: Chain A: E.102, K.105 Chain B: P.384, R.386, S.387 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Water bridges: B:R.386 Hydrogen bonds: A:E.102, A:K.105 GOL.7: 7 residues within 4Å: Chain A: T.159, H.160 Chain B: N.114, A.203 Chain C: K.287, N.289 Ligands: GOL.18 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:K.287, C:N.289, B:N.114 Water bridges: C:T.279 GOL.8: 5 residues within 4Å: Chain A: H.108, S.112, R.113, A.203 Ligands: SO4.13 No protein-ligand interaction detected (PLIP) GOL.16: 8 residues within 4Å: Chain B: K.23, F.24, E.26, S.29, F.30, E.330 Chain C: K.299, K.337 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:E.26, B:S.29, B:E.327, C:K.299 Water bridges: C:K.299, C:R.302 GOL.17: 6 residues within 4Å: Chain B: R.137, E.181, A.184, G.185, V.188, K.459 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.137, B:R.137, B:E.181, B:K.459 GOL.18: 6 residues within 4Å: Chain B: H.108, R.111, S.112, R.113, A.203 Ligands: GOL.7 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.108, B:R.113 GOL.26: 5 residues within 4Å: Chain C: L.148, E.151, A.450, L.453, G.454 1 PLIP interactions: 1 interactions with chain C Water bridges: C:E.151 GOL.27: 3 residues within 4Å: Chain C: R.137, R.141, N.461 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.137, C:R.137, C:R.141, C:R.141, C:N.461 GOL.32: 5 residues within 4Å: Chain D: H.108, S.112, R.113, A.203 Ligands: SO4.24 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:S.112, D:R.113 GOL.33: 2 residues within 4Å: Chain D: S.439, Y.441 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.439 Water bridges: D:E.451, D:E.451 GOL.34: 4 residues within 4Å: Chain D: L.148, E.151, A.450, G.454 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.151

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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