SMTL ID : 9ggi.1 (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

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

SO4.1: 4 residues within 4Å: Chain A: N.356, E.357, D.358, R.359 Ligand excluded by PLIP SO4.2: 6 residues within 4Å: Chain A: T.159, H.160 Chain B: N.114 Chain C: K.287, N.289 Ligands: SO4.9 Ligand excluded by PLIP SO4.3: 4 residues within 4Å: Chain A: S.281, S.282, I.283 Chain C: H.389 Ligand excluded by PLIP SO4.4: 4 residues within 4Å: Chain A: Q.407, G.430, V.431, E.432 Ligand excluded by PLIP SO4.7: 4 residues within 4Å: Chain B: N.356, E.357, D.358, R.359 Ligand excluded by PLIP SO4.8: 5 residues within 4Å: Chain B: S.281, S.282, I.283 Chain D: R.386, H.389 Ligand excluded by PLIP SO4.9: 5 residues within 4Å: Chain B: H.108, R.111, S.112, R.113 Ligands: SO4.2 Ligand excluded by PLIP SO4.10: 2 residues within 4Å: Chain B: T.56, D.57 Ligand excluded by PLIP SO4.11: 3 residues within 4Å: Chain B: K.380, F.428, K.437 Ligand excluded by PLIP SO4.17: 2 residues within 4Å: Chain C: T.56, D.57 Ligand excluded by PLIP SO4.18: 6 residues within 4Å: Chain A: K.287 Chain C: T.159, H.160 Chain D: N.114, A.203 Ligands: SO4.27 Ligand excluded by PLIP SO4.19: 2 residues within 4Å: Chain C: N.356, R.359 Ligand excluded by PLIP SO4.26: 3 residues within 4Å: Chain B: H.389 Chain D: S.281, S.282 Ligand excluded by PLIP SO4.27: 4 residues within 4Å: Chain D: H.108, S.112, R.113 Ligands: SO4.18 Ligand excluded by PLIP SO4.28: 7 residues within 4Å: Chain B: K.287, N.289 Chain C: N.114, A.203 Chain D: T.159, H.160 Ligands: GOL.23 Ligand excluded by PLIP SO4.29: 2 residues within 4Å: Chain D: T.56, D.57 Ligand excluded by PLIP SO4.30: 4 residues within 4Å: Chain D: N.356, E.357, D.358, R.359 Ligand excluded by PLIP SO4.31: 4 residues within 4Å: Chain D: Q.407, G.430, V.431, E.432 Ligand excluded by PLIP SO4.32: 4 residues within 4Å: Chain D: K.32, V.33, Y.35, W.81 Ligand excluded by PLIP

11 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 4 residues within 4Å: Chain A: T.56, S.58, D.59, K.106 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.56, A:K.106 Water bridges: A:T.56, A:S.58, A:D.59, A:D.59 GOL.6: 5 residues within 4Å: Chain A: H.108, S.112, R.113, A.203 Ligands: GOL.13 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.113 Water bridges: A:H.108, A:R.113 GOL.12: 6 residues within 4Å: Chain A: E.178, R.182 Chain B: F.196, M.226, R.227, D.231 10 PLIP interactions: 7 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:R.227, A:E.178, A:E.178, A:R.182 Water bridges: B:R.193, B:R.193, B:P.225, B:R.227, B:N.228, B:D.235 GOL.13: 7 residues within 4Å: Chain A: N.114, Y.321 Chain B: T.159, H.160 Chain D: K.287, N.289 Ligands: GOL.6 3 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: D:N.289, B:T.159, A:N.114 GOL.14: 5 residues within 4Å: Chain B: P.365, Q.407, G.430, V.431, E.432 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Q.407, B:V.431, B:E.432 Water bridges: B:P.365, B:E.405, B:G.430, B:N.433 GOL.20: 4 residues within 4Å: Chain C: S.439, S.440, Y.441, C.448 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.439 GOL.21: 9 residues within 4Å: Chain C: H.108, A.110, R.111, C.202, A.203 Chain D: Q.165, T.372, F.385 Ligands: GOL.23 11 PLIP interactions: 8 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:H.108, C:A.110, C:R.111, C:A.203, D:Q.165 Water bridges: C:H.108, C:A.201, C:L.204, C:G.206, D:Q.165, D:D.376 GOL.22: 5 residues within 4Å: Chain C: W.124, D.127, A.128, T.131, M.340 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:W.124, C:T.131 Water bridges: C:Q.37, C:T.131, C:T.131 GOL.23: 6 residues within 4Å: Chain C: H.108, S.112, R.113, A.203 Ligands: GOL.21, SO4.28 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:H.108, C:R.113 GOL.33: 6 residues within 4Å: Chain D: L.148, E.151, A.450, L.453, G.454, V.457 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:E.151, D:A.450 Water bridges: D:E.151 GOL.34: 4 residues within 4Å: Chain D: S.29, K.32, W.81, T.83 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:K.32, D:K.32 Water bridges: D:W.81, D:W.81, D:T.83, D:T.83

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

CL.15: 5 residues within 4Å: Chain C: S.440, Y.441 Chain D: I.211, D.212, R.213 Ligand excluded by PLIP CL.16: 5 residues within 4Å: Chain C: I.211, D.212, R.213 Chain D: S.440, Y.441 Ligand excluded by PLIP CL.25: 1 residues within 4Å: Chain D: H.51 Ligand excluded by PLIP

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

NA.24: 5 residues within 4Å: Chain C: V.117, R.236, F.325, D.328, K.329 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.236, C:D.328 Water bridges: C:K.329

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

Related Entries With Identical Sequence