SMTL ID : 6pa9.1

E. coli L-asparaginase II mutant (T12V) in complex with L-Asn at pH 7.0

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

homo-tetramer

Ligands

4 x ASN: ASPARAGINE(Non-covalent)

ASN.1: 13 residues within 4Å: Chain A: G.19, V.20, V.35, G.65, S.66, Q.67, G.96, T.97, D.98, A.122, M.123 Chain C: N.256, E.291 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:V.20 Hydrogen bonds: A:V.20, A:S.66, A:Q.67, A:T.97, A:D.98, A:D.98, A:A.122, C:E.291 Water bridges: A:I.21 ASN.2: 11 residues within 4Å: Chain B: G.19, V.20, G.65, S.66, Q.67, G.96, T.97, D.98, A.122 Chain D: N.256, E.291 10 PLIP interactions: 8 interactions with chain B, 1 Ligand-Ligand interactions, 1 interactions with chain D Hydrophobic interactions: B:V.20 Hydrogen bonds: B:V.20, B:S.66, B:Q.67, B:T.97, B:D.98, B:A.122, D:E.291 Water bridges: B:I.21, N.2 ASN.4: 13 residues within 4Å: Chain A: N.256, E.291 Chain C: G.19, V.20, V.35, G.65, S.66, Q.67, G.96, T.97, D.98, A.122, M.123 10 PLIP interactions: 9 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:V.20 Hydrogen bonds: C:V.20, C:S.66, C:Q.67, C:T.97, C:D.98, C:D.98, C:A.122, A:E.291 Water bridges: C:I.21 ASN.5: 11 residues within 4Å: Chain B: N.256, E.291 Chain D: G.19, V.20, G.65, S.66, Q.67, G.96, T.97, D.98, A.122 10 PLIP interactions: 1 Ligand-Ligand interactions, 1 interactions with chain B, 8 interactions with chain D Water bridges: N.5, D:I.21 Hydrogen bonds: B:E.291, D:V.20, D:S.66, D:Q.67, D:T.97, D:D.98, D:A.122 Hydrophobic interactions: D:V.20

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain B: G.18, G.19, V.20, N.63 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.19, B:N.63 Water bridges: B:V.38 GOL.6: 4 residues within 4Å: Chain D: G.18, G.19, V.20, N.63 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:G.19, D:N.63 Water bridges: D:V.38

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
B

C
A

D
B

L-asparaginase 2

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