SMTL ID : 8jkp.1

SP1746 in complex with dTMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x TMP: THYMIDINE-5'-PHOSPHATE(Non-covalent)

TMP.1: 13 residues within 4Å: Chain A: K.62, N.88, H.91, H.117, T.118, D.135, T.168, L.172, F.177, Y.180, T.183 Ligands: GOL.2, FE.4 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:T.118, A:T.168, A:L.172, A:T.183 Hydrogen bonds: A:N.88, A:D.135, A:Y.180 Water bridges: A:R.26, A:K.62, A:K.62, A:R.141, A:E.164 Salt bridges: A:K.62, A:H.91, A:H.117 TMP.7: 13 residues within 4Å: Chain B: K.62, N.88, H.91, H.117, T.118, D.135, T.168, L.172, F.177, Y.180, T.183 Ligands: GOL.8, FE.10 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:T.118, B:T.168, B:L.172, B:T.183 Hydrogen bonds: B:N.88, B:D.135, B:Y.180, B:T.183 Water bridges: B:R.26, B:K.62, B:K.62, B:R.141 Salt bridges: B:K.62, B:H.91, B:H.117

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain A: F.143, Y.171 Ligands: TMP.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.168 Water bridges: A:T.168 GOL.8: 3 residues within 4Å: Chain B: F.143, Y.171 Ligands: TMP.7 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.168

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

FE.3: 5 residues within 4Å: Chain A: H.29, H.58, D.59, D.135 Ligands: FE.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.3 FE.4: 6 residues within 4Å: Chain A: D.59, H.91, H.117, T.118 Ligands: TMP.1, FE.3 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.3, TMP.1 FE.9: 5 residues within 4Å: Chain B: H.29, H.58, D.59, D.135 Ligands: FE.10 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.7, H2O.9 FE.10: 6 residues within 4Å: Chain B: D.59, H.91, H.117, T.118 Ligands: TMP.7, FE.9 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.7, H2O.9, TMP.7

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

SO4.5: 3 residues within 4Å: Chain A: P.23, R.26, K.63 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.26, A:K.63 SO4.6: 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 SO4.11: 3 residues within 4Å: Chain B: P.23, R.26, K.63 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.26, B:K.63 SO4.12: 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

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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