SMTL ID : 5t5c.1

A Novel domain in human EXOG converts apoptotic endonuclease to DNA-repair enzyme

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

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

DC-DT-DG-DA-DC-DG-DT-DG.1: 32 residues within 4Å: Chain A: R.52, F.57, G.76, S.80, R.81, G.82, A.83, P.86, A.87, G.88, K.91, F.111, N.114, S.115, N.119, E.122, M.123, R.126, Y.253, L.254, R.257, K.258, E.260 Ligands: DC-DA-DC-DG-DT-DC-DA-DG.2, DC-DA-DC-DG-DT-DC-DA-DG.2, DC-DA-DC-DG-DT-DC-DA-DG.2, DC-DA-DC-DG-DT-DC-DA-DG.2, DC-DA-DC-DG-DT-DC-DA-DG.2, DC-DA-DC-DG-DT-DC-DA-DG.2, DC-DA-DC-DG-DT-DC-DA-DG.2, DC-DA-DC-DG-DT-DC-DA-DG.2, MG.5 Protein-ligand interaction information (PLIP) not available DC-DT-DG-DA-DC-DG-DT-DG.3: 32 residues within 4Å: Chain B: R.52, K.53, F.57, G.76, S.80, R.81, G.82, A.83, P.86, A.87, G.88, K.91, F.111, N.114, S.115, N.119, E.122, M.123, R.126, Y.253, L.254, R.257, K.258 Ligands: DC-DA-DC-DG-DT-DC-DA-DG.4, DC-DA-DC-DG-DT-DC-DA-DG.4, DC-DA-DC-DG-DT-DC-DA-DG.4, DC-DA-DC-DG-DT-DC-DA-DG.4, DC-DA-DC-DG-DT-DC-DA-DG.4, DC-DA-DC-DG-DT-DC-DA-DG.4, DC-DA-DC-DG-DT-DC-DA-DG.4, DC-DA-DC-DG-DT-DC-DA-DG.4, MG.6 Protein-ligand interaction information (PLIP) not available

2 x DC- DA- DC- DG- DT- DC- DA- DG: DNA (5'-D(P*GP*CP*AP*CP*GP*TP*CP*AP*G)-3')(Non-covalent)

DC-DA-DC-DG-DT-DC-DA-DG.2: 16 residues within 4Å: Chain A: K.56, D.112, S.115, N.119, F.250, L.254, K.258, R.263 Ligands: DC-DT-DG-DA-DC-DG-DT-DG.1, DC-DT-DG-DA-DC-DG-DT-DG.1, DC-DT-DG-DA-DC-DG-DT-DG.1, DC-DT-DG-DA-DC-DG-DT-DG.1, DC-DT-DG-DA-DC-DG-DT-DG.1, DC-DT-DG-DA-DC-DG-DT-DG.1, DC-DT-DG-DA-DC-DG-DT-DG.1, DC-DT-DG-DA-DC-DG-DT-DG.1 Protein-ligand interaction information (PLIP) not available DC-DA-DC-DG-DT-DC-DA-DG.4: 20 residues within 4Å: Chain B: K.53, K.56, F.111, D.112, S.115, N.119, F.250, L.254, K.258, R.263, R.267, K.270 Ligands: DC-DT-DG-DA-DC-DG-DT-DG.3, DC-DT-DG-DA-DC-DG-DT-DG.3, DC-DT-DG-DA-DC-DG-DT-DG.3, DC-DT-DG-DA-DC-DG-DT-DG.3, DC-DT-DG-DA-DC-DG-DT-DG.3, DC-DT-DG-DA-DC-DG-DT-DG.3, DC-DT-DG-DA-DC-DG-DT-DG.3, DC-DT-DG-DA-DC-DG-DT-DG.3 Protein-ligand interaction information (PLIP) not available

2 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 7 residues within 4Å: Chain A: G.82, A.83, N.114, W.118, E.122 Ligands: DC-DT-DG-DA-DC-DG-DT-DG.1, DC-DT-DG-DA-DC-DG-DT-DG.1 No protein-ligand interaction detected (PLIP) MG.6: 7 residues within 4Å: Chain B: G.82, A.83, N.114, W.118, E.122 Ligands: DC-DT-DG-DA-DC-DG-DT-DG.3, DC-DT-DG-DA-DC-DG-DT-DG.3 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Szymanski, M.R. et al., A domain in human EXOG converts apoptotic endonuclease to DNA-repair exonuclease. Nat Commun (2017)

Release Date

2017-05-17

Peptides

Nuclease EXOG, mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Nuclease EXOG, mitochondrial

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