SMTL ID : 3n55.3 (6 other biounits)

SO1698 protein, an aspartic peptidase from Shewanella oneidensis.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.57 Å

Oligo State

homo-dimer

Ligands

2 x PRO- GLN- ILE- ILE- ASN- ARG- PRO: Peptidase(Non-covalent)

PRO-GLN-ILE-ILE-ASN-ARG-PRO.1: 21 residues within 4Å: Chain A: Y.29, Q.38, G.39, D.40, I.41, T.42, V.43, T.44, I.49, I.75, I.76, D.92, K.95, T.96, P.97, G.98, T.99, T.100, K.101, F.102, F.104 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:Y.29, A:I.41, A:T.42, A:V.43, A:I.49, A:I.76, A:K.95, A:P.97, A:F.102, A:F.102 Hydrogen bonds: A:D.40, A:I.41, A:I.41, A:V.43, A:V.43, A:K.95, A:T.96, A:T.96, A:G.98, A:G.98, A:T.100, A:T.100, A:F.102 Water bridges: A:T.96, A:F.102, A:P.118 PRO-GLN-ILE-ILE-ASN-ARG-PRO.5: 21 residues within 4Å: Chain B: Y.29, Q.38, G.39, D.40, I.41, T.42, V.43, T.44, I.49, I.75, I.76, D.92, K.95, T.96, P.97, G.98, T.99, T.100, K.101, F.102, F.104 26 PLIP interactions: 26 interactions with chain B Hydrophobic interactions: B:Y.29, B:I.41, B:T.42, B:V.43, B:I.49, B:I.76, B:K.95, B:P.97, B:F.102, B:F.102 Hydrogen bonds: B:D.40, B:I.41, B:I.41, B:V.43, B:V.43, B:D.92, B:K.95, B:T.96, B:T.96, B:G.98, B:G.98, B:T.100, B:T.100, B:F.102, B:F.102 Water bridges: B:K.95

2 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.2: 4 residues within 4Å: Chain A: C.37, Q.38, G.39, D.40 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.38, A:G.39, A:D.40 Water bridges: A:D.40, A:D.40 BME.6: 4 residues within 4Å: Chain B: C.37, Q.38, G.39, D.40 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.38, B:G.39, B:D.40 Water bridges: B:D.40

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 1 residues within 4Å: Chain A: D.119 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.119 ACT.7: 1 residues within 4Å: Chain B: D.119 1 PLIP interactions: 1 interactions with chain B Water bridges: B:D.119

2 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain A: G.74, D.77, D.94, T.96 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:G.74, A:D.94, A:T.96, H2O.4, H2O.5 ZN.8: 4 residues within 4Å: Chain B: G.74, D.77, D.94, T.96 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:G.74, B:D.94, B:T.96, H2O.10, H2O.10

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Osipiuk, J. et al., Characterization of member of DUF1888 protein family, self-cleaving and self-assembling endopeptidase. J.Biol.Chem. (2012)

Release Date

2010-06-02

Peptides

Peptidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Peptidase

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