SMTL ID : 8h46.1

Blasnase-T13A/P55N with L-asn

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

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

MG.1: 2 residues within 4Å: Chain A: E.268, D.295 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.295, H2O.4, H2O.5, H2O.8 MG.2: 4 residues within 4Å: Chain A: D.218 Chain B: E.207 Ligands: MG.3, MG.11 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.218, H2O.8, H2O.16 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.4, H2O.7 MG.9: 5 residues within 4Å: Chain B: G.219, R.223, N.246, D.250 Ligands: FMT.12 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:N.246, B:D.250, H2O.10 MG.10: 2 residues within 4Å: Chain B: E.268, D.295 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.268, B:D.295, H2O.10, H2O.13 MG.11: 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.2, H2O.16 MG.16: 2 residues within 4Å: Chain C: E.268, D.295 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.295, H2O.22, H2O.23, H2O.26 MG.17: 4 residues within 4Å: Chain C: D.218 Chain D: E.207 Ligands: MG.18, MG.26 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.218, H2O.26, H2O.34 MG.18: 1 residues within 4Å: Ligands: MG.17 No protein-ligand interaction detected (PLIP) MG.19: 3 residues within 4Å: Chain C: N.246, D.250 Ligands: FMT.20 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:N.246, C:D.250, H2O.22, H2O.25 MG.24: 5 residues within 4Å: Chain D: G.219, R.223, N.246, D.250 Ligands: FMT.27 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:N.246, D:D.250, H2O.28 MG.25: 2 residues within 4Å: Chain D: E.268, D.295 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.268, D:D.295, H2O.28, H2O.31 MG.26: 3 residues within 4Å: Chain D: E.207, E.228 Ligands: MG.17 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.207, D:E.207, D:E.228, H2O.20, H2O.34

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

FMT.5: 6 residues within 4Å: Chain A: D.218, G.219, R.223, N.246, D.250 Ligands: MG.4 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.219, A:R.223, A:R.223 Water bridges: A:D.218, A:D.218, A:D.218, A:D.218 FMT.6: 6 residues within 4Å: Chain A: L.292, G.293, K.294, Y.296, F.320, C.321 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.292 Water bridges: A:K.294, A:K.304 FMT.7: 1 residues within 4Å: Chain A: A.286 No protein-ligand interaction detected (PLIP) FMT.12: 6 residues within 4Å: Chain B: D.218, G.219, R.223, N.246, D.250 Ligands: MG.9 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.219, B:R.223, B:R.223 FMT.13: 6 residues within 4Å: Chain A: D.216 Chain B: F.61, P.206, E.207, V.208, R.302 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.208, B:R.302, B:R.302 FMT.20: 6 residues within 4Å: Chain C: D.218, G.219, R.223, N.246, D.250 Ligands: MG.19 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:G.219, C:R.223, C:R.223 Water bridges: C:D.218, C:D.218, C:D.218 FMT.21: 6 residues within 4Å: Chain C: L.292, G.293, K.294, Y.296, F.320, C.321 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:L.292 Water bridges: C:K.294, C:K.304 FMT.22: 1 residues within 4Å: Chain C: A.286 No protein-ligand interaction detected (PLIP) FMT.27: 6 residues within 4Å: Chain D: D.218, G.219, R.223, N.246, D.250 Ligands: MG.24 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:G.219, D:R.223, D:R.223 FMT.28: 6 residues within 4Å: Chain C: D.216 Chain D: F.61, P.206, 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

4 x ASN: ASPARAGINE(Non-covalent)

ASN.8: 13 residues within 4Å: Chain A: G.12, A.13, N.55, S.56, G.88, T.89, D.90, S.114, Q.115 Chain B: Q.242, Y.276, Y.278 Ligands: GOL.14 14 PLIP interactions: 4 interactions with chain B, 10 interactions with chain A Hydrophobic interactions: B:Y.276 Hydrogen bonds: B:Q.242, B:Y.278, B:Y.278, A:A.13, A:N.55, A:S.56, A:T.89, A:D.90, A:S.114 Water bridges: A:I.14, A:D.90, A:D.90, A:K.162 ASN.15: 12 residues within 4Å: Chain A: Q.242, Y.276, Y.278 Chain B: G.12, A.13, N.55, S.56, G.88, T.89, D.90, S.114, Q.115 13 PLIP interactions: 10 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:A.13, B:N.55, B:S.56, B:T.89, B:D.90, B:S.114, A:Q.242, A:Y.278, A:Y.278 Water bridges: B:I.14, B:D.90, B:D.90, B:K.162 ASN.23: 13 residues within 4Å: Chain C: G.12, A.13, N.55, S.56, G.88, T.89, D.90, S.114, Q.115 Chain D: Q.242, Y.276, Y.278 Ligands: GOL.29 14 PLIP interactions: 9 interactions with chain C, 5 interactions with chain D Hydrogen bonds: C:A.13, C:N.55, C:S.56, C:T.89, C:D.90, C:S.114, D:Q.242, D:Y.276, D:Y.278 Water bridges: C:I.14, C:M.57, C:K.162, D:Y.278 Hydrophobic interactions: D:Y.276 ASN.30: 12 residues within 4Å: Chain C: Q.242, Y.276, Y.278 Chain D: G.12, A.13, N.55, S.56, G.88, T.89, D.90, S.114, Q.115 12 PLIP interactions: 3 interactions with chain C, 9 interactions with chain D Hydrogen bonds: C:Q.242, C:Y.278, D:A.13, D:N.55, D:S.56, D:T.89, D:D.90, D:S.114 Water bridges: C:Y.278, D:I.14, D:M.57, D:K.162

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.14: 7 residues within 4Å: Chain A: Q.115, K.162, A.165 Chain B: R.240, T.275, Y.276 Ligands: ASN.8 9 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: B:R.240, B:Y.276, A:Q.115, A:K.162, N.8 Water bridges: B:Y.276, A:Q.120, A:Q.120, N.8 GOL.29: 7 residues within 4Å: Chain C: Q.115, K.162, A.165 Chain D: R.240, T.275, Y.276 Ligands: ASN.23 9 PLIP interactions: 2 Ligand-Ligand interactions, 3 interactions with chain D, 4 interactions with chain C Hydrogen bonds: N.23, D:R.240, D:Y.276, D:Y.276, C:Q.115, C:K.162 Water bridges: N.23, C:Q.120, C:Q.120

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

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