SMTL ID : 4ndf.1 (1 other biounit)

Human Aprataxin (Aptx) bound to RNA-DNA, AMP, and Zn - product complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.94 Å

Oligo State

monomer

Ligands

1 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.1: 18 residues within 4Å: Chain A: G.10, L.11, S.14, I.31, K.32, D.33, K.34, Y.35, K.37, H.41, L.43, H.91, P.94, S.95, M.96, H.100, H.102 Chain B: G.1 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:S.14, A:S.14, A:K.34, A:Y.35, A:K.37, A:S.95, A:M.96 Water bridges: A:S.14, A:K.37, A:K.37, A:H.100, A:H.102 Salt bridges: A:H.91, A:H.100, A:H.102 pi-Stacking: A:Y.35

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.159, C.162, H.175, H.179 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.159, A:C.162, A:H.175, A:H.179

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

NA.3: 1 residues within 4Å: Chain A: S.95 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.95

1 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.4: 6 residues within 4Å: Chain A: Y.35, P.111, C.112, K.114 Chain B: T.2, T.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:C.112

1 x K: POTASSIUM ION(Non-functional Binders)

K.5: 4 residues within 4Å: Chain B: T.8, T.9 Chain C: T.4, C.5 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tumbale, P. et al., Aprataxin resolves adenylated RNA-DNA junctions to maintain genome integrity. Nature (2013)

Release Date

2013-12-18

Peptides

Aprataxin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Aprataxin

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