SMTL ID : 8jjk.1

SP1746 in complex with ADP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

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

ADP.1: 19 residues within 4Å: Chain A: R.26, H.29, D.59, K.62, N.88, H.91, H.117, T.118, D.135, R.141, T.168, L.172, P.178, I.179, Y.180, T.183 Ligands: FE.5, FE.6, MG.7 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:N.88, A:Y.180, A:T.183, A:T.183 Water bridges: A:R.26, A:K.62, A:R.141, A:R.141, A:R.141, A:R.141, A:T.168 Salt bridges: A:R.26, A:H.29, A:K.62, A:K.62, A:H.91, A:H.91, A:H.117, A:R.141 ADP.8: 19 residues within 4Å: Chain B: R.26, H.29, D.59, K.62, N.88, H.91, H.117, T.118, D.135, R.141, T.168, L.172, P.178, I.179, Y.180, T.183 Ligands: FE.12, FE.13, MG.14 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:N.88, B:Y.180, B:T.183 Water bridges: B:R.26, B:K.62, B:R.141, B:R.141, B:R.141, B:R.141, B:T.168 Salt bridges: B:R.26, B:H.29, B:K.62, B:K.62, B:H.91, B:H.91, B:H.117, B:R.141

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: N.188 Chain B: N.84, W.85, P.178 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.84, A:N.188 Water bridges: B:N.84, B:W.85 GOL.3: 4 residues within 4Å: Chain A: P.23, K.25, R.26, K.63 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.25, A:K.25, A:R.26, A:R.26 Water bridges: A:K.25 GOL.4: 3 residues within 4Å: Chain A: E.151, I.152, K.159 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.159 Water bridges: A:K.159 GOL.9: 4 residues within 4Å: Chain A: N.84, W.85, P.178 Chain B: N.188 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.84, B:N.188 Water bridges: A:N.84, A:W.85 GOL.10: 4 residues within 4Å: Chain B: P.23, K.25, R.26, K.63 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.25, B:K.25, B:R.26, B:R.26 Water bridges: B:K.25 GOL.11: 3 residues within 4Å: Chain B: E.151, I.152, K.159 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.151, B:K.159 Water bridges: B:K.159

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

FE.5: 8 residues within 4Å: Chain A: R.26, H.29, H.58, D.59, D.135, R.141 Ligands: ADP.1, FE.6 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.6: 6 residues within 4Å: Chain A: D.59, H.91, H.117, T.118 Ligands: ADP.1, FE.5 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.12: 8 residues within 4Å: Chain B: R.26, H.29, H.58, D.59, D.135, R.141 Ligands: ADP.8, FE.13 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.8 FE.13: 6 residues within 4Å: Chain B: D.59, H.91, H.117, T.118 Ligands: ADP.8, FE.12 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.59, B:H.91, B:H.117, H2O.8

2 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 5 residues within 4Å: Chain A: H.117, Y.132, D.135, E.164 Ligands: ADP.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.117, A:D.135, A:E.164 MG.14: 5 residues within 4Å: Chain B: H.117, Y.132, D.135, E.164 Ligands: ADP.8 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.117, B:D.135, B:E.164

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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