SMTL ID : 6pa2.1

E. coli L-asparaginase II mutant (K162M) in complex with L-Asp at pH 5.6

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

4 x ASP: ASPARTIC ACID(Non-covalent)

ASP.1: 11 residues within 4Å: Chain A: G.19, T.20, G.65, S.66, Q.67, G.96, T.97, D.98, A.122 Chain B: N.256, E.291 13 PLIP interactions: 11 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:T.20, A:T.20, A:S.66, A:Q.67, A:T.97, A:T.97, A:D.98, A:D.98, B:E.291 Water bridges: A:I.21, A:I.21, A:M.123, B:E.291 ASP.2: 12 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, M.123 14 PLIP interactions: 8 interactions with chain B, 4 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, A:N.256, A:E.291 Water bridges: B:I.21, B:M.123, A:E.291, A:E.291, D.2, D.2 ASP.3: 14 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, M.123 Chain D: N.256, E.291 12 PLIP interactions: 9 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, C:D.98, D.3, D.3, D:E.291 Water bridges: C:I.21, C:Y.33 ASP.5: 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 10 PLIP interactions: 7 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, C:E.291, D.5, D.5 Water bridges: D:A.122

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain C: C.113, D.114, K.115, P.116, S.149, A.150, N.151 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:D.114, C:N.151, C:N.151 Water bridges: C:K.115, C:K.115, C:K.115, C:V.117, C:G.153

Links

RCSB   PDBe   PDBe-KB   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
C

C
B

D
D

L-asparaginase 2