SMTL ID : 8jk9.1

SP1746 in complex with GDP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 4 residues within 4Å: Chain A: N.84, W.85, P.178 Chain B: N.188 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.188, A:N.84 GOL.5: 3 residues within 4Å: Chain A: N.88, F.177 Ligands: GDP.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.88 GOL.8: 4 residues within 4Å: Chain A: N.188 Chain B: N.84, W.85, P.178 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.84, A:N.188 GOL.12: 3 residues within 4Å: Chain B: N.88, F.177 Ligands: GDP.11 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.88

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

FE.2: 7 residues within 4Å: Chain A: H.29, H.58, D.59, D.135, R.141 Ligands: FE.3, GDP.4 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.3: 6 residues within 4Å: Chain A: D.59, H.91, H.117, T.118 Ligands: FE.2, GDP.4 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.9: 7 residues within 4Å: Chain B: H.29, H.58, D.59, D.135, R.141 Ligands: FE.10, GDP.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.11 FE.10: 6 residues within 4Å: Chain B: D.59, H.91, H.117, T.118 Ligands: FE.9, GDP.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.11

2 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.4: 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.2, FE.3, GOL.5 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:N.88, A:D.135, A:P.178, A:P.178, A:Y.180, A:T.183 Water bridges: A:R.26, A:R.26, A:K.62, 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, A:R.141 GDP.11: 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.9, FE.10, GOL.12 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:N.88, B:D.135, B:P.178, B:P.178, B:Y.180 Water bridges: B:R.26, B:R.26, B:K.62, 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, B:R.141

4 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 7 residues within 4Å: Chain A: N.88, V.89, H.91, G.92, M.93, T.118 Ligands: MG.7 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:N.88, A:V.89, A:T.118 MG.7: 7 residues within 4Å: Chain A: M.93, E.115, I.116, H.117, T.118, V.119 Ligands: MG.6 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.115 MG.13: 7 residues within 4Å: Chain B: N.88, V.89, H.91, G.92, M.93, T.118 Ligands: MG.14 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:N.88, B:V.89, B:T.118 MG.14: 7 residues within 4Å: Chain B: M.93, E.115, I.116, H.117, T.118, V.119 Ligands: MG.13 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.115

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