SMTL ID : 7ffp.1

Crystal structure of di-peptidase-E from Xenopus laevis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x ASP: ASPARTIC ACID(Non-covalent)

ASP.1: 12 residues within 4Å: Chain A: G.91, G.92, T.94, S.125, A.126, N.129, T.138, N.139, D.140, P.161, H.162 Chain B: E.175 14 PLIP interactions: 3 interactions with chain B, 10 interactions with chain A, 1 Ligand-Ligand interactions Water bridges: B:R.180, B:R.180, B:Q.183 Hydrogen bonds: A:G.92, A:G.92, A:T.94, A:S.125, A:A.126, A:N.129, A:N.139, A:N.139, A:D.140, D.1 Salt bridges: A:H.162 ASP.3: 12 residues within 4Å: Chain A: E.175 Chain B: G.91, G.92, T.94, S.125, A.126, N.129, T.138, N.139, D.140, P.161, H.162 16 PLIP interactions: 12 interactions with chain B, 1 Ligand-Ligand interactions, 3 interactions with chain A Hydrogen bonds: B:G.92, B:G.92, B:T.94, B:T.94, B:S.125, B:A.126, B:N.129, B:T.138, B:N.139, B:N.139, B:D.140, D.3 Salt bridges: B:H.162 Water bridges: A:R.180, A:R.180, A:Q.183

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 3 residues within 4Å: Chain A: S.14, G.91, S.124 No protein-ligand interaction detected (PLIP) CA.4: 3 residues within 4Å: Chain B: S.14, G.91, S.124 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kumar, A. et al., Crystal structure of aspartyl dipeptidase from Xenopus laevis revealed ligand binding induced loop ordering and catalytic triad assembly. Proteins (2022)

Release Date

2021-09-08

Peptides

Alpha-aspartyl dipeptidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Alpha-aspartyl dipeptidase

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