SMTL ID : 5eqv.1

1.45 Angstrom Crystal Structure of Bifunctional 2',3'-cyclic Nucleotide 2'-phosphodiesterase/3'-Nucleotidase Periplasmic Precursor Protein from Yersinia pestis with Phosphate bound to the Active site

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

monomer

Ligands

2 x FE: FE (III) ION(Non-covalent)

FE.1: 6 residues within 4Å: Chain A: D.62, N.102, H.211, H.243 Ligands: FE.2, PO4.5 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.62, A:H.211, A:H.243, H2O.5 FE.2: 6 residues within 4Å: Chain A: D.17, H.19, D.62, H.245 Ligands: FE.1, PO4.5 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.17, A:H.19, A:D.62, A:H.245, H2O.5

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

NA.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NA.4: 1 residues within 4Å: Chain A: S.55 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.55 Water bridges: A:D.94

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

PO4.5: 9 residues within 4Å: Chain A: H.19, D.62, N.102, H.103, H.243, H.245 Ligands: FE.1, FE.2, MLT.6 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.102 Salt bridges: A:H.19, A:H.103, A:H.243, A:H.245

1 x MLT: D-MALATE(Non-covalent)

MLT.6: 5 residues within 4Å: Chain A: N.102, H.103, W.173, E.224 Ligands: PO4.5 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.173 Hydrogen bonds: A:N.102, A:N.102, A:H.243 Salt bridges: A:H.103

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.7: 6 residues within 4Å: Chain A: T.188, E.189, K.192, Y.219, Y.229, Q.232 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.192

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.8: 5 residues within 4Å: Chain A: N.21, D.26, Y.28, F.36, S.67 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.21, A:N.21, A:D.26 Water bridges: A:N.21, A:G.66, A:G.66

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Minasov, G. et al., 1.45 Angstrom Crystal Structure of Bifunctional 2',3'-cyclic Nucleotide 2'-phosphodiesterase/3'-Nucleotidase Periplasmic Precursor Protein from Yersinia pestis with Phosphate bound to the Active site. To Be Published

Release Date

2015-11-25

Peptides

bifunctional 2',3'-cyclic nucleotide 2'-phosphodiesterase/3'-nucleotidase periplasmic precursor protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

bifunctional 2',3'-cyclic nucleotide 2'-phosphodiesterase/3'-nucleotidase periplasmic precursor protein