SMTL ID : 4pvs.1

Crystal structure of fully-cleaved human l-asparaginase protein in complex with l-aspartate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.84 Å

Oligo State

homo-dimer

Ligands

2 x NA: SODIUM ION(Non-functional Binders)

NA.1: 6 residues within 4Å: Chain A: L.57, E.58, D.60, F.63, A.65, C.67 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.63, A:A.65, A:A.65 NA.3: 6 residues within 4Å: Chain B: L.57, E.58, D.60, F.63, A.65, C.67 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.57, B:F.63, B:A.65

2 x ASP: ASPARTIC ACID(Non-covalent)

ASP.2: 10 residues within 4Å: Chain A: T.170, T.188, G.190, I.191, R.198, G.200, D.201, T.221, G.222, G.224 16 PLIP interactions: 15 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:I.191 Hydrogen bonds: A:T.170, A:T.188, A:T.188, A:D.201, A:D.201, A:T.221, A:G.222, A:G.224, D.2 Water bridges: A:N.64, A:N.64, A:T.170, A:G.190, A:G.222 Salt bridges: A:R.198 ASP.4: 10 residues within 4Å: Chain B: T.170, T.188, G.190, R.198, D.201, S.202, T.221, G.222, G.224, I.227 13 PLIP interactions: 12 interactions with chain B, 1 Ligand-Ligand interactions Hydrogen bonds: B:T.170, B:T.170, B:D.201, B:G.222, B:G.222, B:G.224, D.4 Water bridges: B:N.64, B:N.64, B:T.170, B:G.190, B:G.200 Salt bridges: B:R.198

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nomme, J. et al., Structures of apo and product-bound human L-asparaginase: insights into the mechanism of autoproteolysis and substrate hydrolysis. Biochemistry (2012)

Release Date

2014-03-26

Peptides

Isoaspartyl peptidase/L-asparaginase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Isoaspartyl peptidase/L-asparaginase

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