SMTL ID : 7zeh.2 (3 other biounits)

Human cytosolic 5' nucleotidase IIIB in complex with 3,4-diF-Bn7Guanine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

1 x IPQ: N7-(3,4-difluorobenzyl) guanine(Non-covalent)

IPQ.1: 10 residues within 4Å: Chain A: Y.62, L.65, D.66, L.79, W.107, W.108, A.111, H.112, L.115 Ligands: RBL.2 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:W.107, A:W.107, A:W.108, A:W.108 Hydrogen bonds: A:Y.62, A:H.112 Water bridges: A:D.66 Salt bridges: A:D.66 pi-Stacking: A:Y.62, A:Y.62, A:Y.62, A:W.108

1 x RBL: D-ribulose(Post Translational Modification)

RBL.2: 7 residues within 4Å: Chain A: E.90, I.91, W.108, T.204 Ligands: IPQ.1, EDO.6, PO4.9 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:E.90 Water bridges: A:S.233, A:S.233

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

EDO.3: 5 residues within 4Å: Chain A: R.170, K.173, V.174, F.175, H.176 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.169, A:F.175 EDO.4: 3 residues within 4Å: Chain A: I.179, H.180, I.181 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.181, A:Y.185 EDO.5: 5 residues within 4Å: Chain A: H.112, N.113, C.116, G.196, F.197 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.112, A:F.197 Water bridges: A:F.197 EDO.6: 6 residues within 4Å: Chain A: T.204, Y.205, S.233, I.234, G.235 Ligands: RBL.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.204, A:G.235 Water bridges: A:Y.205, A:K.207, A:S.233, A:I.234 EDO.7: 6 residues within 4Å: Chain A: Q.39, I.41, F.155, F.157, S.209, V.243 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.39, A:Q.39, A:S.209

1 x MG: MAGNESIUM ION(Non-covalent)

MG.8: 3 residues within 4Å: Chain A: D.43, D.45, D.232 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.43, A:D.45, A:D.232, H2O.1, H2O.2, H2O.4

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.9: 6 residues within 4Å: Chain A: Y.62, S.158, A.159, T.204, K.207 Ligands: RBL.2 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:A.159, A:T.204 Water bridges: A:D.45, A:D.45, A:K.207, A:K.207 Salt bridges: A:K.207

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

SO4.10: 4 residues within 4Å: Chain A: D.257, K.258, V.259, K.276 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.258, A:V.259 Water bridges: A:E.260, A:K.276, A:K.276 Salt bridges: A:K.276

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kubacka, D. et al., Substrate-Based Design of Cytosolic Nucleotidase IIIB Inhibitors and Structural Insights into Inhibition Mechanism. Pharmaceuticals (2022)

Release Date

2022-05-25

Peptides

7-methylguanosine phosphate-specific 5'-nucleotidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

7-methylguanosine phosphate-specific 5'-nucleotidase

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