SMTL ID : 8bi3.1

Structure of E. coli Class 2 L-asparaginase EcAIII, mutant M200W (crystal M200W#1)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

hetero-2-2-mer

Ligands

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

PEG.1: 5 residues within 4Å: Chain A: F.74, S.145, T.146, S.147, Y.150 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.145 PEG.6: 4 residues within 4Å: Chain B: V.108, L.110, W.121, E.135 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.135 Water bridges: B:Y.123 PEG.7: 4 residues within 4Å: Chain C: F.74, S.145, S.147, Y.150 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.145 PEG.12: 3 residues within 4Å: Chain D: V.108, L.110, W.121 2 PLIP interactions: 2 interactions with chain D Water bridges: D:V.108, D:Y.123

2 x NA: SODIUM ION(Non-functional Binders)

NA.2: 6 residues within 4Å: Chain A: L.60, E.61, C.63, F.66, A.68, I.70 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.60, A:A.68 NA.9: 6 residues within 4Å: Chain C: L.60, E.61, C.63, F.66, A.68, I.70 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:A.68, C:A.68

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 2 residues within 4Å: Chain A: R.17 Chain B: Y.133 Ligand excluded by PLIP CL.4: 5 residues within 4Å: Chain A: H.102, R.138, V.139, S.140, P.141 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain C: L.22, Q.23 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain D: I.132, Y.133 Ligand excluded by PLIP

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

EDO.5: 3 residues within 4Å: Chain B: E.105, N.107, Y.123 2 PLIP interactions: 2 interactions with chain B Water bridges: B:E.105, B:N.107

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.8: 5 residues within 4Å: Chain C: K.3 Chain D: E.105, G.106, N.107, Y.123 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.3

2 x CA: CALCIUM ION(Non-covalent)

CA.11: 1 residues within 4Å: Chain C: D.51 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:D.51, H2O.17, H2O.17, H2O.17, H2O.20 CA.14: 1 residues within 4Å: Chain D: D.126 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:D.126, H2O.22, H2O.24, H2O.24, H2O.25

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Janicki, M. et al., The effects of nature-inspired amino acid substitutions on structural and biochemical properties of the E. coli L-asparaginase EcAIII. Protein Sci. (2023)

Release Date

2023-05-03

Peptides

Isoaspartyl peptidase subunit alpha: AC
Isoaspartyl peptidase subunit beta: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

C
CCC

B
BBB

D
DDD

Isoaspartyl peptidase subunit alpha

Isoaspartyl peptidase subunit beta

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