SMTL ID : 3ovg.5 (5 other biounits)

The crystal structure of an amidohydrolase from Mycoplasma synoviae with Zn ion bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.06 Å

Oligo State

homo-trimer

Ligands

6 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.26, H.28, K.155, D.274 Ligands: ZN.2 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.26, A:H.28, A:D.274, H2O.8, H2O.8 ZN.2: 5 residues within 4Å: Chain A: H.26, K.155, H.188, H.216 Ligands: ZN.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.188, A:H.216, H2O.8 ZN.4: 5 residues within 4Å: Chain B: H.26, K.155, H.188, H.216 Ligands: ZN.5 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.188, B:H.216, H2O.16 ZN.5: 5 residues within 4Å: Chain B: H.26, H.28, K.155, D.274 Ligands: ZN.4 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.26, B:H.28, B:D.274, H2O.16 ZN.7: 5 residues within 4Å: Chain C: H.26, H.28, K.155, D.274 Ligands: ZN.8 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.26, C:H.28, C:D.274, H2O.23, H2O.23 ZN.8: 5 residues within 4Å: Chain C: H.26, K.155, H.188, H.216 Ligands: ZN.7 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.188, C:H.216, H2O.23

3 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 6 residues within 4Å: Chain A: F.43, K.219, K.246, Y.247, R.277, Y.280 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Y.280, A:Y.280 Water bridges: A:K.219, A:K.219, A:D.274 Salt bridges: A:K.219, A:K.246, A:R.277 PO4.6: 5 residues within 4Å: Chain B: F.43, K.246, Y.247, R.277, Y.280 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.280 Salt bridges: B:K.219, B:K.246, B:R.277 PO4.9: 5 residues within 4Å: Chain C: K.219, K.246, Y.247, R.277, Y.280 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:Y.247, C:R.277, C:Y.280 Water bridges: C:K.219, C:K.219 Salt bridges: C:K.219, C:K.246

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, Z. et al., The crystal structure of an amidohydrolase from Mycoplasma synoviae with Zn ion bound. To be Published

Release Date

2010-10-13

Peptides

amidohydrolase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
F

amidohydrolase

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