SMTL ID : 6cvq.1 (1 other biounit)

Human Aprataxin (Aptx) H201Q bound to RNA-DNA, AMP and Zn product complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

monomer

Ligands

1 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.1: 21 residues within 4Å: Chain A: G.10, L.11, S.14, M.20, I.31, K.32, D.33, K.34, Y.35, K.37, Q.41, L.43, H.91, P.94, S.95, M.96, H.100, H.102, F.122 Chain B: G.1, T.2 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:S.14, A:K.34, A:Y.35, A:Y.35, A:Q.41, A:S.95, A:M.96 Water bridges: A:K.34, A:K.37, A:K.37 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: 6 residues within 4Å: Chain A: C.159, E.161, C.162, H.175, K.178, 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: 2 residues within 4Å: Chain A: S.95 Chain B: G.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.95, 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:K.114

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: D.147, G.148, M.149, P.150, E.151 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.147, A:G.148, A:E.151 Water bridges: A:M.149 GOL.6: 5 residues within 4Å: Chain A: Y.23, D.25, E.26, Q.27, H.66 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.23, A:D.25, A:E.26, A:E.26

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

2018-07-04

Peptides

Aprataxin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Aprataxin

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