SMTL ID : 8jkr.1

SP1746 in complex with UMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x U5P: URIDINE-5'-MONOPHOSPHATE(Non-covalent)

U5P.1: 12 residues within 4Å: Chain A: N.88, H.91, H.117, T.118, V.119, D.135, T.168, L.172, Y.180, T.183 Ligands: GOL.6, FE.7 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:T.118, A:T.168, A:L.172 Hydrogen bonds: A:N.88, A:Y.180, A:T.183 Water bridges: A:R.26, A:K.62, A:K.62, A:K.62, A:R.141 Salt bridges: A:K.62, A:H.91, A:H.117 U5P.10: 12 residues within 4Å: Chain B: N.88, H.91, H.117, T.118, V.119, D.135, T.168, L.172, Y.180, T.183 Ligands: GOL.15, FE.16 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:T.118, B:T.168, B:L.172 Hydrogen bonds: B:N.88, B:Y.180 Water bridges: B:R.26, B:K.62, B:K.62, B:K.62, B:R.141 Salt bridges: B:K.62, B:H.91, B:H.117

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

EDO.2: 4 residues within 4Å: Chain A: D.81, Y.180, P.181, Q.182 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.180, A:Q.182 Water bridges: A:Y.180 EDO.3: 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 EDO.11: 4 residues within 4Å: Chain B: D.81, Y.180, P.181, Q.182 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.180, B:Q.182 EDO.12: 4 residues within 4Å: Chain A: N.188 Chain B: N.84, W.85, P.178 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.188, B:N.84

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: Q.123, M.124, K.129, N.158, F.190, Y.193 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.123, A:M.124, A:K.129, A:N.158, A:Y.193 GOL.5: 3 residues within 4Å: Chain A: V.148, E.151, K.159 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.151, A:E.151, A:K.159 GOL.6: 4 residues within 4Å: Chain A: F.143, T.168, Y.171 Ligands: U5P.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.168 GOL.13: 6 residues within 4Å: Chain B: Q.123, M.124, K.129, N.158, F.190, Y.193 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.123, B:M.124, B:K.129, B:N.158 GOL.14: 3 residues within 4Å: Chain B: V.148, E.151, K.159 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.151, B:K.159 GOL.15: 4 residues within 4Å: Chain B: F.143, T.168, Y.171 Ligands: U5P.10 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.168 Water bridges: B:T.168

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

FE.7: 6 residues within 4Å: Chain A: D.59, H.91, H.117, T.118 Ligands: U5P.1, FE.8 6 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: A:D.59, A:H.91, A:H.117, U5P.1, H2O.2, H2O.2 FE.8: 5 residues within 4Å: Chain A: H.29, H.58, D.59, D.135 Ligands: FE.7 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.2, H2O.3 FE.16: 6 residues within 4Å: Chain B: D.59, H.91, H.117, T.118 Ligands: U5P.10, FE.17 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.59, B:H.91, B:H.117, H2O.7, H2O.7 FE.17: 5 residues within 4Å: Chain B: H.29, H.58, D.59, D.135 Ligands: FE.16 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.7

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

SO4.9: 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 SO4.18: 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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