SMTL ID : 6o3p.1

Crystal structure of the catalytic domain of mouse Nudt12 in complex with AMP and 3 Mg2+ ions

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.1: 13 residues within 4Å: Chain A: D.201, A.233, G.234, F.235, E.249, E.253, E.294 Chain B: V.192, N.194, Y.197 Ligands: MG.2, MG.3, MG.4 10 PLIP interactions: 1 interactions with chain B, 9 interactions with chain A pi-Stacking: B:Y.197, A:F.235, A:F.235 Hydrogen bonds: A:R.199, A:D.201, A:A.233, A:F.235, A:E.249 Water bridges: A:R.248, A:R.248 AMP.7: 13 residues within 4Å: Chain A: V.192, N.194, Y.197 Chain B: D.201, A.233, G.234, F.235, E.249, E.253, E.294 Ligands: MG.8, MG.9, MG.10 13 PLIP interactions: 4 interactions with chain A, 9 interactions with chain B Water bridges: A:N.194, A:Y.197, A:Y.197, B:D.201, B:R.248 pi-Stacking: A:Y.197, B:F.235, B:F.235 Hydrogen bonds: B:R.199, B:D.201, B:A.233, B:A.233, B:F.235

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 7 residues within 4Å: Chain A: A.233, G.234, E.249, E.253, E.294 Ligands: AMP.1, MG.3 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:A.233, A:E.253, A:E.294, H2O.1, H2O.2 MG.3: 7 residues within 4Å: Chain A: E.249, E.252, E.253, E.294 Ligands: AMP.1, MG.2, MG.4 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.249, A:E.253, A:E.294, H2O.2, H2O.4 MG.4: 4 residues within 4Å: Chain A: R.248, E.249 Ligands: AMP.1, MG.3 6 PLIP interactions: 1 interactions with chain A, 1 Ligand-Ligand interactions, 4 Ligand-Water interactions Metal complexes: A:E.249, AMP.1, H2O.2, H2O.2, H2O.3, H2O.4 MG.8: 7 residues within 4Å: Chain B: A.233, G.234, E.249, E.253, E.294 Ligands: AMP.7, MG.9 6 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: B:A.233, B:E.253, B:E.294, H2O.7, H2O.7, AMP.7 MG.9: 7 residues within 4Å: Chain B: E.249, E.252, E.253, E.294 Ligands: AMP.7, MG.8, MG.10 6 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: B:E.249, B:E.253, B:E.294, H2O.6, H2O.10, AMP.7 MG.10: 3 residues within 4Å: Chain B: E.249 Ligands: AMP.7, MG.9 6 PLIP interactions: 1 interactions with chain B, 1 Ligand-Ligand interactions, 4 Ligand-Water interactions Metal complexes: B:E.249, AMP.7, H2O.8, H2O.8, H2O.10, H2O.10

2 x ZN: ZINC ION(Non-covalent)

ZN.5: 6 residues within 4Å: Chain A: C.163, C.166, C.181, R.183, C.186, S.188 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.163, A:C.166, A:C.181, A:C.186 ZN.6: 5 residues within 4Å: Chain B: C.163, C.166, C.181, C.186, S.188 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.163, B:C.166, B:C.181, B:C.186

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Grudzien-Nogalska, E. et al., Structural and mechanistic basis of mammalian Nudt12 RNA deNADding. Nat.Chem.Biol. (2019)

Release Date

2019-05-29

Peptides

Peroxisomal NADH pyrophosphatase NUDT12: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Peroxisomal NADH pyrophosphatase NUDT12