SMTL ID : 4ics.1

Crystal structure of PepS from Streptococcus pneumoniae in complex with a substrate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.97 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: E.319, H.381, D.383 Ligands: ZN.2, TRP.3, GLY.4 5 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: A:E.319, A:H.381, A:D.383, TRP.3, H2O.1 ZN.2: 6 residues within 4Å: Chain A: E.253, E.319, A.321, H.348 Ligands: ZN.1, TRP.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.253, A:E.253, A:E.319, A:H.348, H2O.1 ZN.5: 6 residues within 4Å: Chain B: E.319, H.381, D.383 Ligands: ZN.6, TRP.7, GLY.8 5 PLIP interactions: 3 interactions with chain B, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: B:E.319, B:H.381, B:D.383, TRP.7, H2O.10 ZN.6: 6 residues within 4Å: Chain B: E.253, E.319, A.321, H.348 Ligands: ZN.5, TRP.7 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.253, B:E.253, B:E.319, B:H.348, H2O.10

2 x TRP: TRYPTOPHAN(Non-covalent)

TRP.3: 14 residues within 4Å: Chain A: W.144, S.234, A.235, P.247, N.248, T.251, E.253, F.255, E.319, Y.355, H.381 Ligands: ZN.1, ZN.2, GLY.4 8 PLIP interactions: 8 interactions with chain A, Hydrophobic interactions: A:W.144, A:P.247, A:F.255, A:F.255, A:F.255, A:Y.355 Hydrogen bonds: A:Y.355 pi-Stacking: A:Y.355 TRP.7: 14 residues within 4Å: Chain B: W.144, S.234, A.235, P.247, N.248, E.253, F.255, E.319, Y.355, H.381, D.383 Ligands: ZN.5, ZN.6, GLY.8 6 PLIP interactions: 6 interactions with chain B, Hydrophobic interactions: B:P.247, B:P.247, B:F.255, B:F.255 Hydrogen bonds: B:Y.355 pi-Stacking: B:Y.355

2 x GLY: GLYCINE(Non-covalent)

GLY.4: 8 residues within 4Å: Chain A: W.144, V.146, N.248, D.343, Y.355, D.383 Ligands: ZN.1, TRP.3 6 PLIP interactions: 2 Ligand-Ligand interactions, 4 interactions with chain A Water bridges: G.4, G.4 Hydrogen bonds: A:N.248, A:D.343, A:Y.355, A:D.383 GLY.8: 8 residues within 4Å: Chain B: W.144, V.146, N.248, D.343, Y.355, D.383 Ligands: ZN.5, TRP.7 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.248, B:D.343, B:Y.355, B:D.383

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ta, H.M. et al., Structure-based elucidation of the regulatory mechanism for aminopeptidase activity. Acta Crystallogr.,Sect.D (2013)

Release Date

2013-10-23

Peptides

Aminopeptidase PepS: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Aminopeptidase PepS

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