SMTL ID : 8jk5.1

Crystal structure of SP1746 from Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

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

FE.1: 7 residues within 4Å: Chain A: H.58, D.59, H.91, H.117, T.118 Ligands: FE.2, GOL.5 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.59, A:H.91, A:H.117, H2O.1, H2O.3 FE.2: 5 residues within 4Å: Chain A: H.29, H.58, D.59, D.135 Ligands: FE.1 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.29, A:H.58, A:D.59, A:D.135, H2O.1, H2O.1 FE.6: 7 residues within 4Å: Chain B: H.58, D.59, H.91, H.117, T.118 Ligands: FE.7, GOL.10 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.59, B:H.91, B:H.117, H2O.5, H2O.7 FE.7: 5 residues within 4Å: Chain B: H.29, H.58, D.59, D.135 Ligands: FE.6 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.29, B:H.58, B:D.59, B:D.135, H2O.5, H2O.5

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

SO4.3: 3 residues within 4Å: Chain A: R.141, A.142, F.143 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.142, A:F.143 Salt bridges: A:R.141 SO4.4: 3 residues within 4Å: Chain A: G.86, N.87, N.88 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.87, A:N.88 SO4.8: 3 residues within 4Å: Chain B: R.141, A.142, F.143 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.142, B:F.143 Salt bridges: B:R.141 SO4.9: 3 residues within 4Å: Chain B: G.86, N.87, N.88 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.87, B:N.88

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 7 residues within 4Å: Chain A: K.62, N.88, H.91, H.117, T.118, D.135 Ligands: FE.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.88 Water bridges: A:R.26, A:R.26, A:R.141 GOL.10: 7 residues within 4Å: Chain B: K.62, N.88, H.91, H.117, T.118, D.135 Ligands: FE.6 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.88 Water bridges: B:R.26, B:R.26, B:R.141

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jin, Y. et al., Structural and biochemical characterization of a nucleotide hydrolase from Streptococcus pneumonia. Structure (2024)

Release Date

2024-05-08

Peptides

bis(5'-nucleosyl)-tetraphosphatase (symmetrical): AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

bis(5'-nucleosyl)-tetraphosphatase (symmetrical)

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