SMTL ID : 4ojv.1

Crystal structure of unliganded yeast PDE1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.31 Å

Oligo State

homo-dimer

Ligands

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 11 residues within 4Å: Chain A: G.13, H.130, D.132, H.213, D.244, H.294, H.326, K.328 Chain B: W.175 Ligands: ZN.3, ZN.4 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.13 Water bridges: A:H.294 Salt bridges: A:H.130, A:H.213, A:H.294, A:H.326, A:K.328 SO4.5: 11 residues within 4Å: Chain A: W.175 Chain B: G.13, H.130, D.132, H.213, D.244, H.294, H.326, K.328 Ligands: ZN.7, ZN.8 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.13 Water bridges: B:H.294 Salt bridges: B:H.130, B:H.213, B:H.294, B:H.326, B:K.328

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.2: 12 residues within 4Å: Chain A: N.12, P.66, S.67, F.68, Y.69, V.327, K.328, S.329, P.336, R.337 Chain B: R.48, M.111 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.48, A:S.329 Water bridges: B:R.48 Hydrophobic interactions: A:P.336 MPD.6: 12 residues within 4Å: Chain A: R.48, M.111 Chain B: N.12, P.66, S.67, F.68, Y.69, V.327, K.328, S.329, P.336, R.337 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:R.48, B:Y.69, B:S.329 Water bridges: A:R.48 Hydrophobic interactions: B:P.336

4 x ZN: ZINC ION(Non-covalent)

ZN.3: 6 residues within 4Å: Chain A: H.128, H.130, H.213, D.244 Ligands: SO4.1, ZN.4 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.128, A:H.130, A:H.213, A:D.244, H2O.1 ZN.4: 6 residues within 4Å: Chain A: D.132, H.133, D.244, H.326 Ligands: SO4.1, ZN.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.132, A:H.133, A:D.244, A:H.326, H2O.1 ZN.7: 6 residues within 4Å: Chain B: H.128, H.130, H.213, D.244 Ligands: SO4.5, ZN.8 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.128, B:H.130, B:H.213, B:D.244, H2O.10 ZN.8: 6 residues within 4Å: Chain B: D.132, H.133, D.244, H.326 Ligands: SO4.5, ZN.7 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.132, B:H.133, B:D.244, B:H.326, H2O.10

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tian, Y. et al., Dual specificity and novel structural folding of yeast phosphodiesterase-1 for hydrolysis of second messengers cyclic adenosine and guanosine 3',5'-monophosphate. Biochemistry (2014)

Release Date

2014-12-03

Peptides

3',5'-cyclic-nucleotide phosphodiesterase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

3',5'-cyclic-nucleotide phosphodiesterase 1

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