SMTL ID : 8jk8.1

SP1746 in complex with UDP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 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, UDP.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.2 FE.2: 6 residues within 4Å: Chain A: H.29, H.58, D.59, D.135 Ligands: FE.1, UDP.3 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.2 FE.9: 7 residues within 4Å: Chain B: H.58, D.59, H.91, H.117, T.118 Ligands: FE.10, UDP.11 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.59, B:H.91, B:H.117, H2O.6 FE.10: 6 residues within 4Å: Chain B: H.29, H.58, D.59, D.135 Ligands: FE.9, UDP.11 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.6

2 x UDP: URIDINE-5'-DIPHOSPHATE(Non-covalent)

UDP.3: 16 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, I.179, Y.180, T.183 Ligands: FE.1, FE.2 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:L.172 Hydrogen bonds: A:Y.180, A:T.183, A:T.183 Water bridges: A:R.26, A:R.26, A:T.118, 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 UDP.11: 16 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, I.179, Y.180, T.183 Ligands: FE.9, FE.10 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:L.172 Hydrogen bonds: B:Y.180, B:T.183 Water bridges: B:R.26, B:R.26, B:T.118, 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

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

SO4.4: 3 residues within 4Å: Chain A: R.141, A.142, F.143 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:A.142, A:F.143 Water bridges: A:N.140, A:R.141, A:R.141 Salt bridges: A:R.141 SO4.5: 4 residues within 4Å: Chain A: P.23, R.26, K.62, K.63 4 PLIP interactions: 4 interactions with chain A Water bridges: A:K.63, A:K.63 Salt bridges: A:R.26, A:K.63 SO4.6: 3 residues within 4Å: Chain A: G.86, N.87, N.88 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.86, A:G.86, A:N.87, A:N.88, A:N.88 SO4.12: 3 residues within 4Å: Chain B: R.141, A.142, F.143 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:A.142, B:F.143 Water bridges: B:N.140, B:R.141, B:R.141 Salt bridges: B:R.141 SO4.13: 4 residues within 4Å: Chain B: P.23, R.26, K.62, K.63 4 PLIP interactions: 4 interactions with chain B Water bridges: B:K.63, B:K.63 Salt bridges: B:R.26, B:K.63 SO4.14: 3 residues within 4Å: Chain B: G.86, N.87, N.88 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.86, B:G.86, B:N.87, B:N.88, B:N.88

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 4 residues within 4Å: Chain A: N.188 Chain B: N.84, W.85, P.178 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.188 GOL.15: 4 residues within 4Å: Chain A: N.84, W.85, P.178 Chain B: N.188 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.188

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.8: 2 residues within 4Å: Chain A: E.151, K.159 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.159, A:K.159 EDO.16: 2 residues within 4Å: Chain B: E.151, K.159 2 PLIP interactions: 2 interactions with chain B Water bridges: B:K.159, B:K.159

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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