SMTL ID : 8jka.1

SP1746 in complex with AMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: R.141, A.142, F.143 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.140, A:A.142, A:F.143 Salt bridges: A:R.141 SO4.5: 3 residues within 4Å: Chain B: R.141, A.142, F.143 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.140, B:A.142, B:F.143 Salt bridges: B:R.141

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

FE.2: 7 residues within 4Å: Chain A: R.26, H.29, H.58, D.59, D.135 Ligands: FE.3, AMP.4 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.3: 7 residues within 4Å: Chain A: H.58, D.59, H.91, H.117, T.118 Ligands: FE.2, AMP.4 6 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:D.59, A:H.91, A:H.117, H2O.1, H2O.1, AMP.4 FE.6: 7 residues within 4Å: Chain B: R.26, H.29, H.58, D.59, D.135 Ligands: FE.7, AMP.8 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.4, H2O.5 FE.7: 7 residues within 4Å: Chain B: H.58, D.59, H.91, H.117, T.118 Ligands: FE.6, AMP.8 6 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: B:D.59, B:H.91, B:H.117, H2O.5, H2O.5, AMP.8

2 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.4: 13 residues within 4Å: Chain A: N.88, H.91, H.117, T.118, D.135, T.168, L.172, P.178, I.179, Y.180, T.183 Ligands: FE.2, FE.3 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:N.88, A:D.135, A:Y.180, A:T.183, A:T.183 Water bridges: A:R.26, A:R.141 Salt bridges: A:H.91, A:H.117 AMP.8: 13 residues within 4Å: Chain B: N.88, H.91, H.117, T.118, D.135, T.168, L.172, P.178, I.179, Y.180, T.183 Ligands: FE.6, FE.7 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:N.88, B:D.135, B:Y.180, B:T.183 Water bridges: B:R.26, B:R.141 Salt bridges: B:H.91, B:H.117

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)

Related Entries With Identical Sequence