SMTL ID : 8h4b.1

Blasnase-T13A/M57P with L-asn

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

12 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.1: 2 residues within 4Å: Chain A: E.268, D.295 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.268, A:D.295, H2O.4, H2O.5, H2O.7 MG.2: 5 residues within 4Å: Chain A: D.218 Chain B: E.207 Ligands: MG.3, FMT.5, MG.8 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.218, H2O.8, H2O.15 MG.3: 1 residues within 4Å: Ligands: MG.2 No protein-ligand interaction detected (PLIP) MG.4: 3 residues within 4Å: Chain A: N.246, D.250 Ligands: FMT.5 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:N.246, A:D.250, H2O.3, H2O.7 MG.7: 2 residues within 4Å: Chain B: E.268, D.295 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.268, B:D.295, H2O.11, H2O.12, H2O.15 MG.8: 3 residues within 4Å: Chain B: E.207, E.228 Ligands: MG.2 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.207, B:E.207, B:E.228, H2O.6, H2O.15 MG.11: 2 residues within 4Å: Chain C: E.268, D.295 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:E.268, C:D.295, H2O.20, H2O.22, H2O.23 MG.12: 5 residues within 4Å: Chain C: D.218 Chain D: E.207 Ligands: MG.13, FMT.15, MG.18 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.218, H2O.24, H2O.32 MG.13: 1 residues within 4Å: Ligands: MG.12 No protein-ligand interaction detected (PLIP) MG.14: 3 residues within 4Å: Chain C: N.246, D.250 Ligands: FMT.15 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:N.246, C:D.250, H2O.19, H2O.23 MG.17: 2 residues within 4Å: Chain D: E.268, D.295 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:E.268, D:D.295, H2O.27, H2O.29, H2O.32 MG.18: 3 residues within 4Å: Chain D: E.207, E.228 Ligands: MG.12 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.207, D:E.207, D:E.228, H2O.22, H2O.32

6 x FMT: FORMIC ACID(Non-functional Binders)

FMT.5: 7 residues within 4Å: Chain A: D.218, G.219, R.223, N.246, D.250 Ligands: MG.2, MG.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.219, A:R.223, A:R.223, A:N.246 FMT.9: 5 residues within 4Å: Chain A: D.216 Chain B: F.61, E.207, V.208, R.302 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:D.216, B:V.208, B:R.302, B:R.302 FMT.10: 5 residues within 4Å: Chain A: R.240 Chain B: G.88, T.89, S.114, Q.115 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.89, A:R.240 FMT.15: 7 residues within 4Å: Chain C: D.218, G.219, R.223, N.246, D.250 Ligands: MG.12, MG.14 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:G.219, C:R.223, C:R.223, C:N.246 FMT.19: 5 residues within 4Å: Chain C: D.216 Chain D: F.61, E.207, V.208, R.302 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:V.208, D:R.302, D:R.302 FMT.20: 5 residues within 4Å: Chain C: R.240 Chain D: G.88, T.89, S.114, Q.115 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:R.240, D:T.89

2 x ASN: ASPARAGINE(Non-covalent)

ASN.6: 13 residues within 4Å: Chain A: G.12, A.13, P.55, S.56, P.57, G.88, T.89, D.90, S.114, Q.115 Chain B: Q.242, Y.276, Y.278 9 PLIP interactions: 3 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:Q.242, B:Y.276, B:Y.278, A:A.13, A:S.56, A:T.89, A:D.90, A:S.114 Water bridges: A:I.14 ASN.16: 13 residues within 4Å: Chain C: G.12, A.13, P.55, S.56, P.57, G.88, T.89, D.90, S.114, Q.115 Chain D: Q.242, Y.276, Y.278 8 PLIP interactions: 6 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:A.13, C:S.56, C:T.89, C:D.90, C:S.114, D:Q.242, D:Y.276 Water bridges: C:I.14

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lu, F. et al., Structure-based rational design of Bacillus licheniformis L-asparaginase with low/no D-asparaginase activity for a safer enzyme. To Be Published

Release Date

2023-10-18

Peptides

L-asparaginase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

L-asparaginase