SMTL ID : 4gz0.1 (5 other biounits)

Mus Musculus Tdp2-DNA Substrate Analog (5'-6-aminohexanol) Complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.11 Å

Oligo State

monomer

Ligands

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

DC-DC-DG-DA-DA-DT-DT-DC-DG.1: 20 residues within 4Å: Chain A: N.16, D.18, E.48, H.122, S.125, T.126, R.127, D.158, N.160, R.162, W.193, L.201, I.203, Y.207, D.244, H.245 Ligands: 6AH.29, EDO.30, EDO.31, EDO.32 Protein-ligand interaction information (PLIP) not available

25 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 6 residues within 4Å: Chain A: A.218, E.219, E.220, G.221, H.222, L.223 Ligand excluded by PLIP EDO.3: 6 residues within 4Å: Chain A: D.163, W.180, Q.190, Y.191, R.210, R.213 Ligand excluded by PLIP EDO.4: 2 residues within 4Å: Chain A: Y.74, M.100 Ligand excluded by PLIP EDO.5: 2 residues within 4Å: Chain A: L.233 Ligands: EDO.10 Ligand excluded by PLIP EDO.6: 6 residues within 4Å: Chain A: F.95, P.96, N.97, T.98, E.132, R.135 Ligand excluded by PLIP EDO.7: 2 residues within 4Å: Chain A: S.227 Ligands: EDO.11 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain A: C.35, L.38, Y.39, E.234 Ligands: ACT.28 Ligand excluded by PLIP EDO.9: 5 residues within 4Å: Chain A: T.65, L.80, K.82, V.85, F.87 Ligand excluded by PLIP EDO.10: 9 residues within 4Å: Chain A: K.187, H.188, Q.190, Y.191, D.194, A.197, L.230, W.246 Ligands: EDO.5 Ligand excluded by PLIP EDO.11: 3 residues within 4Å: Chain A: T.9 Ligands: EDO.7, ACT.24 Ligand excluded by PLIP EDO.12: 2 residues within 4Å: Chain A: Y.39, D.229 Ligand excluded by PLIP EDO.13: 7 residues within 4Å: Chain A: W.193, D.194, T.195, N.198, N.200, L.201, D.244 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain A: K.196, A.197, N.199, K.235 Ligand excluded by PLIP EDO.15: 3 residues within 4Å: Chain A: L.38, Y.39 Ligands: ACT.24 Ligand excluded by PLIP EDO.16: 6 residues within 4Å: Chain A: T.195, K.196, I.203, P.204, A.205, A.206 Ligand excluded by PLIP EDO.17: 3 residues within 4Å: Chain A: N.24, C.238 Ligands: EDO.21 Ligand excluded by PLIP EDO.18: 3 residues within 4Å: Chain A: G.113, N.114, L.256 Ligand excluded by PLIP EDO.19: 3 residues within 4Å: Chain A: L.233, E.234, K.235 Ligand excluded by PLIP EDO.20: 1 residues within 4Å: Chain A: Q.90 Ligand excluded by PLIP EDO.21: 2 residues within 4Å: Chain A: R.240 Ligands: EDO.17 Ligand excluded by PLIP EDO.22: 3 residues within 4Å: Chain A: G.69, N.70, I.92 Ligand excluded by PLIP EDO.23: 3 residues within 4Å: Chain A: K.235, L.236, G.239 Ligand excluded by PLIP EDO.30: 3 residues within 4Å: Ligands: DC-DC-DG-DA-DA-DT-DT-DC-DG.1, DC-DC-DG-DA-DA-DT-DT-DC-DG.1, EDO.31 Ligand excluded by PLIP EDO.31: 2 residues within 4Å: Ligands: DC-DC-DG-DA-DA-DT-DT-DC-DG.1, EDO.30 Ligand excluded by PLIP EDO.32: 4 residues within 4Å: Chain A: T.126, E.128 Ligands: DC-DC-DG-DA-DA-DT-DT-DC-DG.1, DC-DC-DG-DA-DA-DT-DT-DC-DG.1 Ligand excluded by PLIP

5 x ACT: ACETATE ION(Non-functional Binders)

ACT.24: 7 residues within 4Å: Chain A: S.11, Y.39, S.40, P.41, L.249 Ligands: EDO.11, EDO.15 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.39, A:L.249 Hydrogen bonds: A:S.11 ACT.25: 2 residues within 4Å: Chain A: H.188, D.229 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.229 Salt bridges: A:H.188 ACT.26: 4 residues within 4Å: Chain A: R.30, G.31, S.34, E.234 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.34, A:E.234, A:E.234 ACT.27: 2 residues within 4Å: Chain A: P.26, Y.56 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.26 Water bridges: A:Y.56 ACT.28: 7 residues within 4Å: Chain A: Y.39, L.230, V.231, G.232, L.233, E.234 Ligands: EDO.8 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.39, A:V.231 Hydrogen bonds: A:Y.39, A:G.232, A:L.233, A:E.234

1 x 6AH: 6-aminohexan-1-ol(Non-covalent)

6AH.29: 5 residues within 4Å: Chain A: E.48, S.125 Ligands: DC-DC-DG-DA-DA-DT-DT-DC-DG.1, DC-DC-DG-DA-DA-DT-DT-DC-DG.1, DC-DC-DG-DA-DA-DT-DT-DC-DG.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.125, A:S.125

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schellenberg, M.J. et al., Mechanism of repair of 5'-topoisomerase II-DNA adducts by mammalian tyrosyl-DNA phosphodiesterase 2. Nat.Struct.Mol.Biol. (2012)

Release Date

2012-10-31

Peptides

Tyrosyl-DNA phosphodiesterase 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Tyrosyl-DNA phosphodiesterase 2

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