SMTL ID : 6b09.1

Crystal structure of HsNUDT16 in complex with diADPR (soaked)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

homo-dimer

Ligands

2 x C7G: [(2~{R},3~{S},4~{S},5~{S})-5-(6-aminopurin-9-yl)-4-[(2~{S},3~{S},4~{S},5~{S})-5-[[[[(2~{R},3~{R},4~{S},5~{S})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-3,4-bis(oxidanyl)oxolan-2-yl]oxy-3-oxidanyl-oxolan-2-yl]methyl phosphono hydrogen phosphate(Non-covalent)

C7G.1: 23 residues within 4Å: Chain A: R.20, V.22, H.24, R.50, F.51, 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, R.38, D.150 Ligands: MG.2, MG.3, NA.5 14 PLIP interactions: 10 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:R.50, A:F.61, A:E.76, A:E.136, A:S.166, A:S.166, A:Q.170, B:R.38, B:D.150, B:D.150, B:D.150 Salt bridges: A:R.20, A:H.24, A:R.50 C7G.6: 21 residues within 4Å: Chain A: F.36, R.149, D.150 Chain B: V.22, H.24, R.50, G.59, G.60, F.61, E.76, E.80, P.104, A.108, E.136, I.164, G.165, S.166, A.167, Q.170 Ligands: MG.7, MG.8 13 PLIP interactions: 5 interactions with chain A, 8 interactions with chain B Hydrogen bonds: A:R.149, A:R.149, A:D.150, A:D.150, B:F.61, B:E.136, B:S.166, B:Q.170, B:Q.170 Salt bridges: A:R.149, B:H.24, B:R.50 pi-Cation interactions: B:H.24

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: R.50, G.59, E.80, E.136 Ligands: C7G.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.80 MG.3: 7 residues within 4Å: Chain A: E.76, E.79, E.80, D.132, E.136 Ligands: C7G.1, NA.5 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.76, A:E.80, A:E.136 MG.7: 3 residues within 4Å: Chain B: R.75, E.76 Ligands: C7G.6 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.76 MG.8: 5 residues within 4Å: Chain B: E.76, E.80, D.132, E.136 Ligands: C7G.6 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.76, B:E.80, B:D.132

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

CL.4: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

2 x NA: SODIUM ION(Non-functional Binders)

NA.5: 4 residues within 4Å: Chain A: E.76, E.79 Ligands: C7G.1, MG.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.76 NA.9: 4 residues within 4Å: Chain B: D.31, G.33, P.40, R.42 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.33, B:R.42

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

2019-01-09

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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