SMTL ID : 6pab.1 (1 other biounit)

E. coli L-asparaginase II in complex with L-Asp at pH 7.0

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.73 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, V.35, G.65, S.66, Q.67, G.96, T.97, D.98, A.122 Chain B: N.256, E.291 14 PLIP interactions: 11 interactions with chain A, 2 Ligand-Ligand interactions, 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, D.1, D.1, B:E.291 Water bridges: A:I.21, A:Y.33, A:K.170, A:K.170 Salt bridges: A:K.170 ASP.4: 11 residues within 4Å: Chain A: N.256, E.291 Chain B: G.19, T.20, 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.4, D.4 Water bridges: B:I.21 Salt bridges: B:K.170 ASP.5: 13 residues within 4Å: Chain C: G.19, T.20, Y.33, V.35, G.65, S.66, Q.67, G.96, T.97, D.98, A.122 Chain D: N.256, E.291 13 PLIP interactions: 10 interactions with chain C, 2 Ligand-Ligand interactions, 1 interactions with chain D Hydrogen bonds: C:T.20, C:T.20, C:S.66, C:Q.67, C:T.97, C:D.98, D.5, D.5, D:E.291 Water bridges: C:I.21, C:K.170, C:K.170 Salt bridges: C:K.170 ASP.8: 11 residues within 4Å: Chain C: N.256, E.291 Chain D: G.19, T.20, G.65, S.66, Q.67, G.96, T.97, D.98, A.122 12 PLIP interactions: 9 interactions with chain D, 1 interactions with chain C, 2 Ligand-Ligand interactions Hydrogen bonds: D:T.20, D:T.20, D:S.66, D:Q.67, D:T.97, D:D.98, D:D.98, C:E.291, D.8, D.8 Water bridges: D:I.21 Salt bridges: D:K.170

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

CIT.2: 5 residues within 4Å: Chain A: K.221, Y.244 Chain B: S.232, D.233, L.234 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:K.221, A:K.221, B:D.233, B:D.233 Water bridges: A:Y.244, A:Y.244 Salt bridges: A:K.221 Hydrophobic interactions: B:L.234 CIT.6: 5 residues within 4Å: Chain C: K.221, Y.244 Chain D: S.232, D.233, L.234 8 PLIP interactions: 4 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:K.221, C:K.221, C:Y.244, D:D.233, D:D.233, D:D.233 Salt bridges: C:K.221 Hydrophobic interactions: D:L.234

2 x IMD: IMIDAZOLE(Non-covalent)

IMD.3: 7 residues within 4Å: Chain A: N.11, I.12, T.13, N.55, K.57, K.87, T.88 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.13 IMD.7: 7 residues within 4Å: Chain C: N.11, I.12, T.13, N.55, K.57, K.87, T.88 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.88

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Lubkowski, J. et al., Geometric considerations support the double-displacement catalytic mechanism of l-asparaginase. Protein Sci. (2019)

Release Date

2019-09-04

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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