SMTL ID : 8ecd.1 (1 other biounit)

E. coli L-asparaginase II mutant (V27T) in complex with L-Asp

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.62 Å

Oligo State

homo-tetramer

Ligands

4 x ASP: ASPARTIC ACID(Non-covalent)

ASP.1: 13 residues within 4Å: Chain A: G.19, T.20, Y.33, T.35, G.65, S.66, Q.67, G.96, T.97, D.98, A.122 Chain B: N.256, E.291 16 PLIP interactions: 13 interactions with chain A, 1 interactions with chain B, 2 Ligand-Ligand interactions Hydrogen bonds: A:T.20, A:T.20, A:T.35, A:T.35, A:S.66, A:Q.67, A:T.97, A:D.98, B:E.291, D.1, D.1 Water bridges: A:I.21, A:Y.33, A:K.170, A:K.170 Salt bridges: A:K.170 ASP.5: 12 residues within 4Å: Chain A: N.256, E.291 Chain B: G.19, T.20, T.35, G.65, S.66, Q.67, G.96, T.97, D.98, A.122 12 PLIP interactions: 9 interactions with chain B, 1 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: B:T.20, B:T.20, B:S.66, B:Q.67, B:T.97, B:D.98, B:D.98, A:E.291, D.5, D.5 Water bridges: B:I.21 Salt bridges: B:K.170 ASP.9: 13 residues within 4Å: Chain C: G.19, T.20, Y.33, T.35, G.65, S.66, Q.67, G.96, T.97, D.98, A.122 Chain D: N.256, E.291 14 PLIP interactions: 1 interactions with chain D, 11 interactions with chain C, 2 Ligand-Ligand interactions Hydrogen bonds: D:E.291, C:T.20, C:T.20, C:T.35, C:S.66, C:Q.67, C:T.97, C:D.98, D.9, D.9 Water bridges: C:I.21, C:K.170, C:K.170 Salt bridges: C:K.170 ASP.13: 12 residues within 4Å: Chain C: N.256, E.291 Chain D: G.19, T.20, T.35, G.65, S.66, Q.67, G.96, T.97, D.98, A.122 14 PLIP interactions: 10 interactions with chain D, 2 Ligand-Ligand interactions, 2 interactions with chain C Hydrogen bonds: D:T.20, D:T.20, D:T.35, D:S.66, D:Q.67, D:T.97, D:D.98, D:D.98, D.13, D.13, C:E.291 Water bridges: D:I.21, C:E.291 Salt bridges: D:K.170

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 9 residues within 4Å: Chain A: Q.288, D.294, A.295, G.298, F.299, V.300, P.324, Q.325, Q.328 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.288, A:G.298 GOL.6: 8 residues within 4Å: Chain B: Q.288, D.294, A.295, G.298, F.299, P.324, Q.325, Q.328 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.288, B:G.298 Water bridges: B:A.295, B:G.298 GOL.7: 4 residues within 4Å: Chain B: F.262, D.263, A.266, Y.297 1 PLIP interactions: 1 interactions with chain B Water bridges: B:Y.297 GOL.10: 9 residues within 4Å: Chain C: Q.288, D.294, A.295, G.298, F.299, V.300, P.324, Q.325, Q.328 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.288, C:G.298 GOL.14: 8 residues within 4Å: Chain D: Q.288, D.294, A.295, G.298, F.299, P.324, Q.325, Q.328 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Q.288, D:G.298 Water bridges: D:A.295, D:G.298 GOL.15: 4 residues within 4Å: Chain D: F.262, D.263, A.266, Y.297 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:D.263, D:Y.297 Water bridges: D:Y.297

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 10 residues within 4Å: Chain A: S.181, N.183, G.185 Chain C: S.181, V.182, N.183, Y.184, G.185, P.186 Ligands: EDO.11 No protein-ligand interaction detected (PLIP) EDO.4: 4 residues within 4Å: Chain A: Q.60, V.61, V.62, N.63 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.63, A:N.63 EDO.8: 11 residues within 4Å: Chain B: S.181, V.182, N.183, G.185 Chain D: S.181, V.182, N.183, Y.184, G.185, P.186 Ligands: EDO.16 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:V.182, D:G.185, B:S.181 EDO.11: 10 residues within 4Å: Chain A: S.181, V.182, N.183, Y.184, G.185, P.186 Chain C: S.181, N.183, G.185 Ligands: EDO.3 No protein-ligand interaction detected (PLIP) EDO.12: 4 residues within 4Å: Chain C: Q.60, V.61, V.62, N.63 2 PLIP interactions: 2 interactions with chain C Water bridges: C:N.63, C:N.63 EDO.16: 11 residues within 4Å: Chain B: S.181, V.182, N.183, Y.184, G.185, P.186 Chain D: S.181, V.182, N.183, G.185 Ligands: EDO.8 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:V.182, B:G.185, D:S.181

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Strzelczyk, P. et al., The E. coli L-asparaginase V27T mutant: structural and functional characterization and comparison with theoretical predictions. Febs Lett. (2022)

Release Date

2022-11-16

Peptides

L-asparaginase 2: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

L-asparaginase 2

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