SMTL ID : 3szq.1

Structure of an S. pombe APTX/DNA/AMP/Zn complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-dimer

Ligands

2 x DC- DC- DC- DT- DG: 5'-D(*CP*CP*CP*TP*G)-3'(Non-covalent)

DC-DC-DC-DT-DG.1: 16 residues within 4Å: Chain A: F.8, F.39, K.41, S.116, M.117, K.135, H.139 Chain B: T.9, C.10, A.11, G.12, G.13, G.14 Chain D: A.7 Ligands: AMP.2, BME.4 Protein-ligand interaction information (PLIP) not available DC-DC-DC-DT-DG.6: 16 residues within 4Å: Chain B: A.7 Chain C: F.8, F.39, K.41, S.116, M.117, K.135, H.139 Chain D: T.9, C.10, A.11, G.12, G.13, G.14 Ligands: AMP.7, BME.9 Protein-ligand interaction information (PLIP) not available

2 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.2: 15 residues within 4Å: Chain A: L.12, Y.15, D.37, M.38, F.39, K.41, H.45, L.47, H.112, P.115, S.116, M.117, H.121, H.123 Ligands: DC-DC-DC-DT-DG.1 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:Y.15, A:Y.15, A:M.38, A:F.39, A:K.41, A:H.45, A:S.116, A:M.117 Water bridges: A:N.11, A:N.11, A:K.41, A:H.112, A:H.112, A:H.112, A:H.112, A:S.116 Salt bridges: A:H.112, A:H.121, A:H.123 pi-Stacking: A:F.39 AMP.7: 15 residues within 4Å: Chain C: L.12, Y.15, D.37, M.38, F.39, K.41, H.45, L.47, H.112, P.115, S.116, M.117, H.121, H.123 Ligands: DC-DC-DC-DT-DG.6 17 PLIP interactions: 17 interactions with chain C Hydrogen bonds: C:Y.15, C:M.38, C:F.39, C:K.41, C:H.45, C:S.116, C:M.117 Water bridges: C:N.11, C:N.11, C:K.41, C:H.112, C:H.112, C:S.116 Salt bridges: C:H.112, C:H.121, C:H.123 pi-Stacking: C:F.39

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

BME.3: 5 residues within 4Å: Chain A: K.108, V.109, K.150, I.151, D.152 No protein-ligand interaction detected (PLIP) BME.4: 5 residues within 4Å: Chain A: S.116, A.138, H.139, S.142 Ligands: DC-DC-DC-DT-DG.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.116, A:S.116 Water bridges: A:S.116 BME.8: 5 residues within 4Å: Chain C: K.108, V.109, K.150, I.151, D.152 No protein-ligand interaction detected (PLIP) BME.9: 5 residues within 4Å: Chain C: S.116, A.138, H.139, S.142 Ligands: DC-DC-DC-DT-DG.6 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.116, C:S.116 Water bridges: C:S.116

2 x ZN: ZINC ION(Non-covalent)

ZN.5: 4 residues within 4Å: Chain A: C.174, C.177, H.191, E.195 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.174, A:C.177, A:H.191, A:E.195 ZN.10: 4 residues within 4Å: Chain C: C.174, C.177, H.191, E.195 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.174, C:C.177, C:H.191, C:E.195

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tumbale, P. et al., Structure of an aprataxin-DNA complex with insights into AOA1 neurodegenerative disease. Nat.Struct.Mol.Biol. (2011)

Release Date

2011-10-12

Peptides

Aprataxin-like protein: AC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

Aprataxin-like protein