SMTL ID : 2xsq.1

Crystal structure of human Nudix motif 16 (NUDT16) in complex with IMP and magnesium

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.72 Å

Oligo State

homo-dimer

Ligands

2 x IMP: INOSINIC ACID(Non-covalent)

IMP.1: 11 residues within 4Å: Chain A: V.44, H.46, R.72, F.73, G.78, F.79, F.83, V.128, I.186, A.189, Q.192 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:F.79, A:Q.192, A:Q.192 Water bridges: A:H.46, A:H.46, A:R.72, A:R.72, A:R.72, A:S.188, A:S.188 Salt bridges: A:R.72 pi-Stacking: A:H.46, A:H.46 IMP.5: 11 residues within 4Å: Chain B: V.44, H.46, R.72, F.73, G.78, F.79, F.83, V.128, I.186, A.189, Q.192 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:F.79, B:Q.192, B:Q.192 Water bridges: B:R.72, B:R.72, B:R.72, B:S.188, B:S.188 Salt bridges: B:R.72 pi-Stacking: B:H.46, B:H.46

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: G.81, E.102 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:G.81, A:E.102, H2O.5, H2O.5, H2O.5 MG.3: 1 residues within 4Å: Chain A: E.98 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:E.98, H2O.4, H2O.5, H2O.5, H2O.8, H2O.8 MG.6: 2 residues within 4Å: Chain B: G.81, E.102 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:G.81, B:E.102, H2O.14, H2O.14, H2O.14 MG.7: 1 residues within 4Å: Chain B: E.98 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:E.98, H2O.13, H2O.14, H2O.14, H2O.17, H2O.17

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 2 residues within 4Å: Chain A: R.60, R.171 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain B: R.60, R.171 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tresaugues, L. et al., Structural Basis for the Specificity of Human Nudt16 and its Regulation by Inosine Monophosphate. Plos One (2015)

Release Date

2010-11-17

Peptides

U8 SNORNA-DECAPPING ENZYME: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

U8 SNORNA-DECAPPING ENZYME

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