SMTL ID : 4gz0.3 (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: 18 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.26, EDO.27 Protein-ligand interaction information (PLIP) not available

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

EDO.2: 6 residues within 4Å: Chain A: N.175, F.177, F.216, R.217, A.218, E.219 Ligand excluded by PLIP EDO.3: 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.4: 2 residues within 4Å: Chain A: Y.39, D.229 Ligand excluded by PLIP EDO.5: 6 residues within 4Å: Chain A: F.95, P.96, N.97, T.98, E.132, R.135 Ligand excluded by PLIP EDO.6: 5 residues within 4Å: Chain A: D.149, T.151, R.217, A.218, E.219 Ligand excluded by PLIP EDO.7: 8 residues within 4Å: Chain A: K.187, H.188, Q.190, Y.191, D.194, A.197, L.230, W.246 Ligand excluded by PLIP EDO.8: 3 residues within 4Å: Chain A: S.34, A.37, L.38 Ligand excluded by PLIP EDO.9: 1 residues within 4Å: Ligands: ACT.23 Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain A: G.19, L.20, G.22, I.50 Ligand excluded by PLIP EDO.11: 2 residues within 4Å: Chain A: G.221, I.224 Ligand excluded by PLIP EDO.12: 4 residues within 4Å: Chain A: K.185, K.187, Q.190 Ligands: EDO.19 Ligand excluded by PLIP EDO.13: 3 residues within 4Å: Chain A: H.188, S.227, L.228 Ligand excluded by PLIP EDO.14: 2 residues within 4Å: Chain A: E.181, F.182 Ligand excluded by PLIP EDO.15: 6 residues within 4Å: Chain A: C.35, Y.39, V.231, G.232, L.233, E.234 Ligand excluded by PLIP EDO.16: 6 residues within 4Å: Chain A: D.163, W.180, Q.190, R.210, R.213 Ligands: EDO.19 Ligand excluded by PLIP EDO.17: 4 residues within 4Å: Chain A: C.169, G.171, L.172, P.173 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain A: N.114, S.150, T.152, E.219, H.222 Ligand excluded by PLIP EDO.19: 4 residues within 4Å: Chain A: D.163, K.185 Ligands: EDO.12, EDO.16 Ligand excluded by PLIP EDO.20: 3 residues within 4Å: Chain A: T.65, I.67, F.87 Ligand excluded by PLIP EDO.21: 5 residues within 4Å: Chain A: N.199, R.202, C.238, G.239, R.240 Ligand excluded by PLIP EDO.27: 2 residues within 4Å: 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

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

ACT.22: 5 residues within 4Å: Chain A: T.65, L.80, K.82, V.85, F.87 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.80, A:F.87 Hydrogen bonds: A:T.65, A:L.80 Water bridges: A:G.83 ACT.23: 5 residues within 4Å: Chain A: S.11, Y.39, P.41, L.249 Ligands: EDO.9 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.249 ACT.24: 3 residues within 4Å: Chain A: K.58, I.66, T.68 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.68 Water bridges: A:T.68 Salt bridges: A:K.58 ACT.25: 4 residues within 4Å: Chain A: R.162, D.163, K.208, H.209 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.163, A:K.208 Water bridges: A:Q.164, A:R.210 Salt bridges: A:H.209

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

6AH.26: 4 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 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.125 Water bridges: A:N.16, A:D.244

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
E

Tyrosyl-DNA phosphodiesterase 2

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