SMTL ID : 2zal.1

Crystal structure of E. coli isoaspartyl aminopeptidase/L-asparaginase in complex with L-aspartate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-2-2-mer

Ligands

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

NA.1: 6 residues within 4Å: Chain A: L.59, E.60, C.62, F.65, A.67, I.69 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:C.62, A:A.67 NA.11: 6 residues within 4Å: Chain C: L.59, E.60, C.62, F.65, A.67, I.69 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:L.59, C:A.67

5 x CA: CALCIUM ION(Non-covalent)

CA.2: 2 residues within 4Å: Chain A: E.136 Ligands: ASP.3 4 PLIP interactions: 2 interactions with chain A, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: A:E.136, A:E.136, ASP.3, H2O.3 CA.4: 4 residues within 4Å: Chain B: G.75 Ligands: CA.6, ASP.9, ASP.10 5 PLIP interactions: 3 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: ASP.9, ASP.10, ASP.10, H2O.5, H2O.5 CA.5: 1 residues within 4Å: Chain B: D.10 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.10, H2O.1, H2O.5, H2O.5 CA.6: 4 residues within 4Å: Chain B: G.75 Ligands: CA.4, ASP.9, ASP.10 5 PLIP interactions: 1 interactions with chain B, 3 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: B:G.75, ASP.9, ASP.9, ASP.10, H2O.4 CA.7: 1 residues within 4Å: Chain B: D.10 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.10

5 x ASP: ASPARTIC ACID(Non-covalent)

ASP.3: 5 residues within 4Å: Chain A: R.103, G.134, M.135, E.136 Ligands: CA.2 8 PLIP interactions: 6 Ligand-Ligand interactions, 2 interactions with chain A Hydrogen bonds: D.3, D.3, D.3, D.3, A:E.136 Water bridges: D.3, D.3, A:N.104 ASP.8: 9 residues within 4Å: Chain B: T.1, G.21, M.22, R.29, D.32, S.33, T.52, G.53, G.55 14 PLIP interactions: 9 interactions with chain B, 4 Ligand-Ligand interactions, 1 interactions with chain A Hydrogen bonds: B:T.1, B:D.32, B:T.52, B:G.53, B:G.53, B:G.55, D.8, D.8, D.8, D.8 Water bridges: B:T.1, B:G.31, A:A.11 Salt bridges: B:R.29 ASP.9: 4 residues within 4Å: Chain B: G.75 Ligands: CA.4, CA.6, ASP.10 4 PLIP interactions: 3 Ligand-Ligand interactions, 1 interactions with chain B Hydrogen bonds: D.10, B:M.71 Water bridges: D.9, D.10 ASP.10: 7 residues within 4Å: Chain B: G.75, L.76, S.77, E.105 Ligands: CA.4, CA.6, ASP.9 7 PLIP interactions: 3 interactions with chain B, 4 Ligand-Ligand interactions Hydrogen bonds: B:L.76, D.10, D.10 Water bridges: B:S.77, B:S.77, D.9, D.10 ASP.15: 9 residues within 4Å: Chain D: T.1, G.21, M.22, R.29, D.32, S.33, T.52, G.53, G.55 13 PLIP interactions: 7 interactions with chain D, 4 interactions with chain C, 2 Ligand-Ligand interactions Hydrogen bonds: D:T.1, D:D.32, D:G.53, D:G.53, D:G.55, D.15, D.15 Water bridges: D:G.31, C:A.11, C:A.11, C:N.66, C:N.66 Salt bridges: D:R.29

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.12: 2 residues within 4Å: Chain C: L.21, Q.22 Ligand excluded by PLIP

2 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.13: 4 residues within 4Å: Chain A: N.128 Chain C: R.75, D.76 Chain D: P.27 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.128, A:N.128 TRS.14: 8 residues within 4Å: Chain C: K.92, A.93, V.112, M.113, S.116, P.117, H.118, V.119 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:A.93, C:A.93, C:P.117, C:H.118

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Michalska, K. et al., Crystal structure of isoaspartyl aminopeptidase in complex with L-aspartate. J.Biol.Chem. (2005)

Release Date

2007-10-30

Peptides

L-asparaginase: AC
L-asparaginase: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

L-asparaginase

L-asparaginase