SMTL ID : 6cvo.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

2 x DA- DA- DC- DA- DG- DC: DNA (5'-D(*AP*AP*CP*AP*GP*C)-3')(Non-functional Binders)(Non-covalent)

DA-DA-DC-DA-DG-DC.1: 6 residues within 4Å: Chain D: G.17, C.18, T.19, G.20, T.21, T.22 4 PLIP interactions: 4 interactions with chain A pi-Stacking: A:W.7, A:W.7, A:W.7 pi-Cation interactions: A:W.7 DA-DA-DC-DA-DG-DC.2: 7 residues within 4Å: Chain B: G.17, C.18, T.19, G.20, T.21, T.22 Chain C: H.6 Protein-ligand interaction information (PLIP) not available

2 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.3: 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 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:S.14, A:K.34, A:Y.35, A:K.37, A:S.95, A:M.96 Water bridges: A:H.91 Salt bridges: A:H.91, A:H.100, A:H.102 pi-Stacking: A:Y.35 AMP.6: 18 residues within 4Å: Chain C: 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 D: G.1 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:S.14, C:K.34, C:Y.35, C:S.95, C:M.96 Water bridges: C:K.37, C:S.95, C:S.95 Salt bridges: C:H.91, C:H.100, C:H.102 pi-Stacking: C:Y.35

2 x ZN: ZINC ION(Non-covalent)

ZN.4: 5 residues within 4Å: Chain A: C.159, E.161, 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 ZN.7: 5 residues within 4Å: Chain C: C.159, E.161, C.162, H.175, H.179 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.159, C:C.162, C:H.175, C:H.179

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

BME.5: 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:K.114 BME.8: 6 residues within 4Å: Chain C: Y.35, P.111, C.112, K.114 Chain D: T.2, T.3 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.114

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tumbale, P. et al., Mechanism of APTX nicked DNA sensing and pleiotropic inactivation in neurodegenerative disease. EMBO J. (2018)

Release Date

2018-08-29

Peptides

Aprataxin: AC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
B

Aprataxin

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