SMTL ID : 6scx.2 (1 other biounit)

Crystal structure of the catalytic domain of human NUDT12 in complex with 7-methyl-guanosine-5'-triphosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.92 Å

Oligo State

homo-dimer

Ligands

4 x CD: CADMIUM ION(Non-covalent)

CD.1: 4 residues within 4Å: Chain A: C.174, C.177, C.192, C.197 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.174, A:C.177, A:C.192, A:C.197 CD.2: 4 residues within 4Å: Chain A: A.244, E.264, E.305 Ligands: MGP.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.264 CD.4: 4 residues within 4Å: Chain B: C.174, C.177, C.192, C.197 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.174, B:C.177, B:C.192, B:C.197 CD.5: 4 residues within 4Å: Chain B: A.244, E.264, E.305 Ligands: MGP.6 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.264

2 x MGP: 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

MGP.3: 12 residues within 4Å: Chain A: D.212, V.214, Q.232, R.234, A.244, G.245, F.246, M.287 Chain B: V.203, N.205, Y.208 Ligands: CD.2 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.232, A:R.234, A:R.234, A:A.244, A:F.246 pi-Stacking: A:F.246 pi-Cation interactions: B:Y.208 MGP.6: 12 residues within 4Å: Chain A: V.203, N.205, Y.208 Chain B: D.212, V.214, Q.232, R.234, A.244, G.245, F.246, M.287 Ligands: CD.5 7 PLIP interactions: 1 interactions with chain A, 6 interactions with chain B pi-Cation interactions: A:Y.208 Hydrogen bonds: B:Q.232, B:R.234, B:R.234, B:A.244, B:F.246 pi-Stacking: B:F.246

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, H. et al., Decapping Enzyme NUDT12 Partners with BLMH for Cytoplasmic Surveillance of NAD-Capped RNAs. Cell Rep (2019)

Release Date

2020-01-08

Peptides

Peroxisomal NADH pyrophosphatase NUDT12: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
C

Peroxisomal NADH pyrophosphatase NUDT12

Related Entries With Identical Sequence