SMTL ID : 5w6x.1

Crystal structure of the HsNUDT16 in complex with Mg+2 and ADP-ribose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x APR: ADENOSINE-5-DIPHOSPHORIBOSE(Non-covalent)

APR.1: 18 residues within 4Å: Chain A: V.22, H.24, R.50, G.59, G.60, F.61, E.76, E.80, A.108, E.136, I.164, G.165, S.166, A.167, Q.170 Chain B: F.36 Ligands: MG.2, MG.3 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:F.61, A:E.76, A:S.166, A:A.167, A:Q.170, A:Q.170 Water bridges: A:R.50, A:R.50, A:R.50, A:R.50, A:G.59, A:S.102, A:S.102 Salt bridges: A:H.24, A:R.50 APR.5: 18 residues within 4Å: Chain A: F.36 Chain B: V.22, H.24, R.50, F.51, G.59, G.60, F.61, E.76, E.80, A.108, I.164, G.165, S.166, A.167, Q.170 Ligands: MG.6, MG.7 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:R.50, B:F.61, B:S.166, B:A.167, B:Q.170, B:Q.170 Salt bridges: B:H.24, B:R.50

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: G.59, E.76, E.80, E.136 Ligands: APR.1, MG.3 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.76, A:E.80, A:E.136, H2O.2, H2O.3 MG.3: 5 residues within 4Å: Chain A: G.59, G.60, E.80 Ligands: APR.1, MG.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:G.59, A:E.80, H2O.5, H2O.5 MG.6: 6 residues within 4Å: Chain B: G.59, E.76, E.80, D.132 Ligands: APR.5, MG.7 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.80, H2O.8 MG.7: 4 residues within 4Å: Chain B: G.59, E.80 Ligands: APR.5, MG.6 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:G.59, B:E.80, H2O.10

2 x ACY: ACETIC ACID(Non-functional Binders)

ACY.4: 1 residues within 4Å: Chain A: L.13 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.21 ACY.8: 6 residues within 4Å: Chain B: L.81, G.82, E.83, A.84, G.126, R.129 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:E.83, B:A.84 Hydrogen bonds: B:E.83, B:A.84 Water bridges: B:G.126, B:G.126 Salt bridges: B:R.129

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.9: 6 residues within 4Å: Chain B: P.30, P.32, R.114, L.115, T.116, L.117 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:P.30, B:R.114

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thirawatananond, P. et al., Structural analyses of NudT16-ADP-ribose complexes direct rational design of mutants with improved processing of poly(ADP-ribosyl)ated proteins. Sci Rep (2019)

Release Date

2018-12-19

Peptides

U8 snoRNA-decapping enzyme: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

U8 snoRNA-decapping enzyme

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