SMTL ID : 6pa5.1 (1 other biounit)

ECAII(T89V,K162T) MUTANT IN COMPLEX WITH L-ASN AT PH 8.3 IN SPACE GROUP P2(1)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

4 x ASN: ASPARAGINE(Non-covalent)

ASN.1: 14 residues within 4Å: Chain A: G.19, T.20, Y.33, V.35, G.65, S.66, Q.67, G.96, V.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 Hydrogen bonds: A:T.20, A:T.20, A:S.66, A:Q.67, A:V.97, A:D.98, A:A.122, C:E.291 Water bridges: A:I.21, A:Y.33 ASN.4: 13 residues within 4Å: Chain B: G.19, T.20, Y.33, V.35, G.65, S.66, Q.67, G.96, V.97, D.98, A.122 Chain D: N.256, E.291 13 PLIP interactions: 11 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:T.20, B:T.20, B:Y.33, B:S.66, B:Q.67, B:Q.67, B:V.97, B:D.98, B:D.98, B:A.122, D:N.256, D:E.291 Water bridges: B:I.21 ASN.7: 12 residues within 4Å: Chain A: N.256, E.291 Chain C: G.19, T.20, G.65, S.66, Q.67, G.96, V.97, D.98, A.122, M.123 9 PLIP interactions: 8 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:T.20, C:T.20, C:S.66, C:Q.67, C:V.97, C:D.98, C:A.122, A:E.291 Water bridges: C:I.21 ASN.9: 12 residues within 4Å: Chain B: N.256, E.291 Chain D: G.19, T.20, G.65, S.66, Q.67, G.96, V.97, D.98, A.122, M.123 11 PLIP interactions: 9 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:T.20, D:T.20, D:S.66, D:Q.67, D:V.97, D:D.98, D:D.98, D:A.122, B:E.291 Water bridges: D:I.21, B:E.291

4 x IMD: IMIDAZOLE(Non-covalent)

IMD.2: 6 residues within 4Å: Chain A: N.11, I.12, T.13, N.55, K.57, T.88 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.12 IMD.5: 7 residues within 4Å: Chain B: N.11, I.12, T.13, N.55, K.57, K.87, T.88 No protein-ligand interaction detected (PLIP) IMD.8: 7 residues within 4Å: Chain C: N.11, I.12, T.13, N.55, K.57, K.87, T.88 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.88 pi-Cation interactions: C:K.57 IMD.10: 7 residues within 4Å: Chain D: N.11, I.12, T.13, N.55, K.57, K.87, T.88 1 PLIP interactions: 1 interactions with chain D pi-Cation interactions: D:K.57

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 2 residues within 4Å: Chain A: D.289, A.290 No protein-ligand interaction detected (PLIP) GOL.6: 2 residues within 4Å: Chain B: D.289, A.290 No protein-ligand interaction detected (PLIP) GOL.11: 2 residues within 4Å: Chain D: S.128, M.129 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain D Hydrogen bonds: A:Y.138, D:M.129 Water bridges: D:S.128, D:M.129

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
C

D
D

L-asparaginase 2

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