SMTL ID : 7c9b.1

Crystal structure of dipeptidase-E from Xenopus laevis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-dimer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: N.129, T.138, N.139, P.161 No protein-ligand interaction detected (PLIP) CA.5: 4 residues within 4Å: Chain B: N.129, T.138, N.139, P.161 No protein-ligand interaction detected (PLIP)

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

NA.2: 3 residues within 4Å: Chain A: G.92, D.140 Chain B: E.175 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.125, A:S.125 Water bridges: A:G.92, B:R.180, B:R.180 NA.3: 5 residues within 4Å: Chain A: T.132, S.134, T.137, N.158, I.159 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.132, A:N.158, A:I.159, A:I.159 Water bridges: A:T.137 NA.4: 3 residues within 4Å: Chain A: K.82, A.109, K.112 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.109, A:R.113 NA.6: 3 residues within 4Å: Chain A: E.175 Chain B: G.92, D.140 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:E.175, B:S.125 Water bridges: A:R.180, A:R.180, B:G.92 NA.7: 5 residues within 4Å: Chain B: T.132, S.134, T.137, N.158, I.159 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.132, B:N.158, B:I.159 Water bridges: B:T.137 NA.8: 3 residues within 4Å: Chain B: K.82, A.109, K.112 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.109, B:R.113

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

2021-06-09

Peptides

Alpha-aspartyl dipeptidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Alpha-aspartyl dipeptidase

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