SMTL ID : 6pae.1

Dickeya chrysanthemi complex with L-Asp at pH 5.6

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-tetramer

Ligands

4 x ASP: ASPARTIC ACID(Non-covalent)

ASP.1: 10 residues within 4Å: Chain A: G.14, T.15, A.61, S.62, E.63, G.94, T.95, D.96, A.120 Chain C: S.254 14 PLIP interactions: 11 interactions with chain A, 2 Ligand-Ligand interactions, 1 interactions with chain C Hydrogen bonds: A:T.15, A:T.15, A:S.62, A:E.63, A:T.95, A:D.96, D.1, D.1, C:S.254 Water bridges: A:G.14, A:G.14, A:I.16, A:K.168 Salt bridges: A:K.168 ASP.7: 11 residues within 4Å: Chain B: G.14, T.15, A.61, S.62, E.63, G.94, T.95, D.96, A.120, M.121 Chain D: S.254 13 PLIP interactions: 12 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:T.15, B:T.15, B:S.62, B:E.63, B:E.63, B:T.95, B:D.96, B:D.96, D:S.254 Water bridges: B:G.14, B:I.16, B:K.168 Salt bridges: B:K.168 ASP.8: 10 residues within 4Å: Chain A: S.254 Chain C: G.14, T.15, A.61, S.62, E.63, G.94, T.95, D.96, A.120 14 PLIP interactions: 11 interactions with chain C, 2 Ligand-Ligand interactions, 1 interactions with chain A Hydrogen bonds: C:T.15, C:T.15, C:S.62, C:E.63, C:T.95, C:D.96, D.8, D.8, A:S.254 Water bridges: C:G.14, C:G.14, C:I.16, C:K.168 Salt bridges: C:K.168 ASP.10: 11 residues within 4Å: Chain B: S.254 Chain D: G.14, T.15, A.61, S.62, E.63, G.94, T.95, D.96, A.120, M.121 12 PLIP interactions: 11 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:T.15, D:T.15, D:S.62, D:E.63, D:E.63, D:T.95, D:D.96, D:D.96, B:S.254 Water bridges: D:G.14, D:I.16 Salt bridges: D:K.168

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

EDO.2: 2 residues within 4Å: Chain A: K.243 Ligands: EDO.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.243 Water bridges: A:K.243 EDO.3: 3 residues within 4Å: Chain A: K.243 Ligands: EDO.2, EDO.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.243 EDO.4: 4 residues within 4Å: Chain A: G.241, K.243 Ligands: EDO.3, EDO.5 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.243 Hydrogen bonds: A:K.243 EDO.5: 6 residues within 4Å: Chain A: K.243, K.269, G.270, V.271 Ligands: EDO.4, EDO.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.243 EDO.6: 3 residues within 4Å: Chain A: K.269, G.270 Ligands: EDO.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.243, A:G.270

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 5 residues within 4Å: Chain C: F.57, S.58, M.60, V.69, K.72 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:F.57, C:K.72, C:K.72

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: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

L-asparaginase

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