SMTL ID : 8ecd.2 (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 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:T.20, A:T.20, A:S.66, A:Q.67, A:T.97, A:D.98, A:D.98, B:E.291 Water bridges: A:T.20, A:I.21, A:Y.33 Salt bridges: A:K.170 ASP.11: 13 residues within 4Å: Chain A: N.256, E.291 Chain B: G.19, T.20, Y.33, T.35, G.65, S.66, Q.67, G.96, T.97, D.98, A.122 14 PLIP interactions: 11 interactions with chain B, 1 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: B:T.20, B:T.20, B:T.35, B:T.35, B:S.66, B:Q.67, B:T.97, B:D.98, A:E.291, D.11, D.11 Water bridges: B:I.21, B:K.170 Salt bridges: B:K.170 ASP.18: 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 13 PLIP interactions: 12 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:T.20, C:T.20, C:T.35, C:S.66, C:Q.67, C:T.97, C:D.98, C:D.98, D:E.291 Water bridges: C:T.20, C:I.21, C:Y.33 Salt bridges: C:K.170 ASP.28: 13 residues within 4Å: Chain C: N.256, E.291 Chain D: G.19, T.20, Y.33, T.35, G.65, S.66, Q.67, G.96, T.97, D.98, A.122 14 PLIP interactions: 2 Ligand-Ligand interactions, 11 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D.28, D.28, D:T.20, D:T.20, D:Y.33, D:T.35, D:S.66, D:Q.67, D:T.97, D:D.98, C:E.291 Water bridges: D:I.21, D:K.170 Salt bridges: D:K.170

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 8 residues within 4Å: Chain A: Q.288, D.294, A.295, G.298, F.299, P.324, Q.325, Q.328 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.288 Water bridges: A:G.298, A:Q.329 GOL.12: 8 residues within 4Å: Chain B: Q.288, D.294, A.295, G.298, F.299, P.324, Q.325, Q.328 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.288, B:G.298, B:P.324 Water bridges: B:A.295, B:G.298 GOL.15: 3 residues within 4Å: Chain B: F.262, D.263, Y.297 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.297 Water bridges: B:K.259, B:K.259 GOL.17: 6 residues within 4Å: Chain A: N.230, Y.258 Chain B: N.70, D.71, N.72 Ligands: CIT.10 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:D.71, B:N.72, A:N.230 Water bridges: B:N.70, B:N.72, B:N.72, A:Y.258 GOL.19: 8 residues within 4Å: Chain C: Q.288, D.294, A.295, G.298, F.299, P.324, Q.325, Q.328 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.288 Water bridges: C:G.298, C:Q.329 GOL.29: 8 residues within 4Å: Chain D: Q.288, D.294, A.295, G.298, F.299, P.324, Q.325, Q.328 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:Q.288, D:G.298, D:P.324 Water bridges: D:A.295, D:G.298 GOL.32: 3 residues within 4Å: Chain D: F.262, D.263, Y.297 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:D.263, D:Y.297, D:Y.297 Water bridges: D:K.259, D:K.259 GOL.34: 6 residues within 4Å: Chain C: N.230, Y.258 Chain D: N.70, D.71, N.72 Ligands: CIT.27 7 PLIP interactions: 4 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:D.71, D:N.72, C:N.230 Water bridges: D:N.70, D:N.72, C:Y.258, C:Y.258

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

EDO.3: 5 residues within 4Å: Chain A: N.172, T.174, D.175 Chain B: G.284 Chain D: Y.189 Ligand excluded by PLIP EDO.4: 7 residues within 4Å: Chain A: K.180, S.181, Y.189 Chain C: V.182, N.183 Ligands: EDO.6, EDO.23 Ligand excluded by PLIP EDO.5: 2 residues within 4Å: Chain A: P.210, Y.334 Ligand excluded by PLIP EDO.6: 14 residues within 4Å: Chain A: S.181, V.182, N.183, Y.184, G.185, P.186 Chain C: S.181, V.182, N.183, Y.184, G.185 Ligands: EDO.4, EDO.21, EDO.23 Ligand excluded by PLIP EDO.7: 7 residues within 4Å: Chain A: N.230, A.231, S.232, D.233, Y.258, S.260 Ligands: CIT.10 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain A: L.318, T.319, Q.320, T.321, K.322 Ligand excluded by PLIP EDO.13: 6 residues within 4Å: Chain A: N.32 Chain B: D.289, A.290, E.291, V.292, D.293 Ligand excluded by PLIP EDO.14: 2 residues within 4Å: Chain B: P.210, Y.334 Ligand excluded by PLIP EDO.16: 12 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, Y.184, G.185 Ligands: EDO.33 Ligand excluded by PLIP EDO.20: 5 residues within 4Å: Chain B: Y.189 Chain C: N.172, T.174, D.175 Chain D: G.284 Ligand excluded by PLIP EDO.21: 7 residues within 4Å: Chain A: V.182, N.183 Chain C: K.180, S.181, Y.189 Ligands: EDO.6, EDO.23 Ligand excluded by PLIP EDO.22: 2 residues within 4Å: Chain C: P.210, Y.334 Ligand excluded by PLIP EDO.23: 14 residues within 4Å: Chain A: S.181, V.182, N.183, Y.184, G.185 Chain C: S.181, V.182, N.183, Y.184, G.185, P.186 Ligands: EDO.4, EDO.6, EDO.21 Ligand excluded by PLIP EDO.24: 7 residues within 4Å: Chain C: N.230, A.231, S.232, D.233, Y.258, S.260 Ligands: CIT.27 Ligand excluded by PLIP EDO.25: 5 residues within 4Å: Chain C: L.318, T.319, Q.320, T.321, K.322 Ligand excluded by PLIP EDO.30: 6 residues within 4Å: Chain C: N.32 Chain D: D.289, A.290, E.291, V.292, D.293 Ligand excluded by PLIP EDO.31: 2 residues within 4Å: Chain D: P.210, Y.334 Ligand excluded by PLIP EDO.33: 12 residues within 4Å: Chain B: S.181, V.182, N.183, Y.184, G.185 Chain D: S.181, V.182, N.183, Y.184, G.185, P.186 Ligands: EDO.16 Ligand excluded by PLIP

4 x CIT: CITRIC ACID(Non-functional Binders)

CIT.9: 5 residues within 4Å: Chain A: K.221, Y.244 Chain B: S.232, D.233, L.234 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:D.233, B:D.233 Water bridges: B:D.233, B:S.260, A:Y.244, A:Y.244 Salt bridges: A:K.221, A:K.221 CIT.10: 7 residues within 4Å: Chain A: S.232, D.233, L.234 Chain B: K.221, Y.244 Ligands: EDO.7, GOL.17 8 PLIP interactions: 3 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:D.233, A:D.233 Water bridges: A:D.233, B:K.221, B:K.221, B:K.221 Salt bridges: B:K.221, B:K.221 CIT.26: 5 residues within 4Å: Chain C: K.221, Y.244 Chain D: S.232, D.233, L.234 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:D.233, C:Y.244 Water bridges: D:D.233, D:S.260 Salt bridges: C:K.221, C:K.221 CIT.27: 7 residues within 4Å: Chain C: S.232, D.233, L.234 Chain D: K.221, Y.244 Ligands: EDO.24, GOL.34 10 PLIP interactions: 4 interactions with chain C, 6 interactions with chain D Hydrogen bonds: C:D.233, C:D.233, C:D.233, D:Y.244 Water bridges: C:D.233, D:K.221, D:K.221, D:K.221 Salt bridges: D:K.221, D:K.221

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
C

B
D

C
C

D
D

L-asparaginase 2

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