SMTL ID : 6x7u.1

Crystal Structure of the Human Nudix Hydrolase Nudt16 in complex with FAD

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-dimer

Ligands

1 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.1: 20 residues within 4Å: Chain A: A.22, H.24, R.50, F.51, G.56, F.57, G.59, G.60, F.61, E.80, V.106, I.164, S.166, A.167, Q.170 Chain B: F.36, R.38, L.148 Ligands: MN.2, MN.3 13 PLIP interactions: 9 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:F.57, A:F.57, A:F.61, A:Q.170, B:R.38 Salt bridges: A:H.24, A:R.50, A:R.50 pi-Stacking: A:H.24, A:H.24, B:F.36, B:F.36 Hydrophobic interactions: B:F.36

4 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 4 residues within 4Å: Chain A: G.59, E.80 Ligands: FAD.1, MN.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:G.59, A:E.80 MN.3: 3 residues within 4Å: Chain A: E.76 Ligands: FAD.1, MN.2 No protein-ligand interaction detected (PLIP) MN.4: 2 residues within 4Å: Chain A: H.99, E.173 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.99, A:E.173, A:E.173 MN.6: 4 residues within 4Å: Chain B: G.59, G.60, E.80 Ligands: AMP.5 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:G.59, B:E.80, AMP.5

1 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.5: 14 residues within 4Å: Chain B: A.22, H.24, R.50, G.56, F.57, G.59, G.60, F.61, V.106, I.164, S.166, A.167, Q.170 Ligands: MN.6 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:R.50, B:F.57, B:F.57, B:Q.170 Salt bridges: B:H.24, B:R.50 pi-Stacking: B:H.24, B:H.24

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sharma, S. et al., Mammalian Nudix proteins cleave nucleotide metabolite caps on RNAs. Nucleic Acids Res. (2020)

Release Date

2020-07-01

Peptides

U8 snoRNA-decapping enzyme: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

U8 snoRNA-decapping enzyme