SMTL ID : 4o0f.1

Crystal structure of the human L-asparaginase protein T219A mutant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.92 Å

Oligo State

homo-dimer

Ligands

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

NA.1: 6 residues within 4Å: Chain A: L.56, E.57, D.59, F.62, A.64, C.66 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.56, A:F.62, A:A.64 NA.2: 5 residues within 4Å: Chain A: G.12, L.167, G.168, T.169, G.221 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:G.12, A:T.169, A:G.221 Water bridges: G.3 NA.5: 7 residues within 4Å: Chain B: L.56, E.57, D.59, P.60, F.62, A.64, C.66 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.57, B:F.62, B:A.64 NA.6: 6 residues within 4Å: Chain B: G.11, G.12, G.168, T.169, A.220, G.221 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.12, B:T.169, B:G.221, B:G.221

4 x GLY: GLYCINE(Non-covalent)

GLY.3: 10 residues within 4Å: Chain A: T.169, T.187, G.189, I.190, R.197, D.200, S.201, G.221, H.222, G.223 10 PLIP interactions: 8 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: A:T.169, A:T.187, A:T.187, A:G.221, A:G.221, A:G.223 Water bridges: A:G.199, G.3, G.3 Salt bridges: A:R.197 GLY.4: 9 residues within 4Å: Chain A: S.89, A.90, V.109, M.110, T.113, P.114, H.115, C.116 Chain B: K.228 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Salt bridges: B:K.228 Hydrogen bonds: A:S.89, A:A.90, A:V.109 GLY.7: 8 residues within 4Å: Chain A: K.228 Chain B: S.89, A.90, V.109, M.110, T.113, H.115, C.116 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:A.90, B:A.90, B:M.110 Salt bridges: A:K.228 GLY.8: 8 residues within 4Å: Chain B: T.169, T.187, G.189, I.190, R.197, D.200, G.221, G.223 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.221, B:G.221, B:G.221, B:G.223 Water bridges: B:G.199 Salt bridges: B:R.197

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nomme, J. et al., Elucidation of the Specific Function of the Conserved Threonine Triad Responsible for Human l-Asparaginase Autocleavage and Substrate Hydrolysis. J.Mol.Biol. (2014)

Release Date

2014-04-30

Peptides

Isoaspartyl peptidase/L-asparaginase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Isoaspartyl peptidase/L-asparaginase