SMTL ID : 8yt5.1

SP1746 treated with EDTA, in complex with ADP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 17 residues within 4Å: Chain A: R.26, H.29, D.59, K.62, 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 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:N.88, A:Y.180, A:T.183 Water bridges: A:R.26, A:R.26, A:R.26, A:K.62, A:K.62, A:R.141, A:R.141 Salt bridges: A:R.26, A:H.29, A:K.62, A:K.62, A:H.91, A:H.91, A:H.117 ADP.4: 17 residues within 4Å: Chain B: R.26, H.29, D.59, K.62, N.88, H.91, H.117, T.118, D.135, T.168, L.172, P.178, I.179, Y.180, T.183 Ligands: FE.5, FE.6 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:N.88, B:Y.180, B:T.183, B:T.183 Water bridges: B:R.26, B:R.26, B:R.26, B:K.62, B:K.62, B:R.141, B:R.141 Salt bridges: B:R.26, B:H.29, B:K.62, B:K.62, B:H.91, B:H.91, B:H.117

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

FE.2: 6 residues within 4Å: Chain A: D.59, H.91, H.117, T.118 Ligands: ADP.1, FE.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.59, A:H.91, A:H.117, H2O.1 FE.3: 6 residues within 4Å: Chain A: H.29, H.58, D.59, D.135 Ligands: ADP.1, FE.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.29, A:H.58, A:D.59, A:D.135, H2O.1 FE.5: 6 residues within 4Å: Chain B: D.59, H.91, H.117, T.118 Ligands: ADP.4, FE.6 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.59, B:H.91, B:H.117, H2O.9 FE.6: 6 residues within 4Å: Chain B: H.29, H.58, D.59, D.135 Ligands: ADP.4, FE.5 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.29, B:H.58, B:D.59, B:D.135, H2O.9

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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