SMTL ID : 9daf.1

L-asparaginase II (EcA2-K12)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-tetramer

Ligands

4 x ASP: ASPARTIC ACID(Non-covalent)

ASP.1: 13 residues within 4Å: Chain A: G.11, T.12, Y.25, V.27, G.57, S.58, Q.59, G.88, T.89, D.90, A.114 Chain C: N.248, E.283 13 PLIP interactions: 12 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:T.12, A:T.12, A:S.58, A:Q.59, A:T.89, A:D.90, C:E.283 Water bridges: A:T.12, A:I.13, A:Y.25, A:D.90, A:K.162 Salt bridges: A:K.162 ASP.3: 14 residues within 4Å: Chain B: G.11, T.12, Y.25, V.27, G.57, S.58, Q.59, G.88, T.89, D.90, A.114, M.115 Chain D: N.248, E.283 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:T.12, B:T.12, B:S.58, B:Q.59, B:Q.59, B:T.89, B:D.90, D:N.248 Water bridges: B:I.13, B:I.13 ASP.6: 12 residues within 4Å: Chain A: N.248, E.283 Chain C: G.11, T.12, V.27, G.57, S.58, Q.59, G.88, T.89, D.90, A.114 9 PLIP interactions: 8 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:T.12, C:T.12, C:S.58, C:T.89, C:D.90, C:D.90, A:E.283 Water bridges: C:K.162 Salt bridges: C:K.162 ASP.8: 13 residues within 4Å: Chain B: N.248, E.283 Chain D: G.11, T.12, Y.25, V.27, G.57, S.58, Q.59, G.88, T.89, D.90, A.114 12 PLIP interactions: 11 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:T.12, D:T.12, D:S.58, D:Q.59, D:Q.59, D:T.89, D:D.90, D:D.90, B:E.283 Water bridges: D:I.13, D:I.13 Salt bridges: D:K.162

1 x ACY: ACETIC ACID(Non-functional Binders)

ACY.2: 9 residues within 4Å: Chain A: V.103, C.105, D.106, K.107, P.108, V.109, G.145, V.146, T.198 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.103, A:V.109, A:V.146, A:T.198 Hydrogen bonds: A:C.105, A:V.109 Water bridges: A:G.145

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 8 residues within 4Å: Chain A: R.116, S.122, V.168 Chain B: D.124, N.128, M.150, N.151, V.168 8 PLIP interactions: 3 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:R.116, A:R.116, A:S.122, B:D.124, B:N.128, B:N.151, B:N.151 Water bridges: B:V.168 PEG.5: 10 residues within 4Å: Chain B: V.244, G.245, R.272, V.273, P.274 Chain D: D.90, E.93, T.161, K.162, Q.300 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain B Hydrogen bonds: D:T.161, D:Q.300, B:G.245, B:R.272, B:R.272 PEG.7: 10 residues within 4Å: Chain A: I.216, V.217, Y.218, P.227 Chain C: I.216, V.217, Y.218, Y.220, S.224, P.227 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:Y.218, C:Y.220, C:S.224, A:Y.218 Water bridges: A:Y.218

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

de Araujo, T.S. et al., Biochemical and Biophysical Divergences between Two Escherichia coli l-Asparaginase II Variants: Potential for Using EcA2-K12 as a Biosimilar. Biochemistry (2025)

Release Date

2025-05-21

Peptides

L-asparaginase 2: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

L-asparaginase 2

Related Entries With Identical Sequence