SMTL ID : 4gz0.2 (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: 17 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.27 Protein-ligand interaction information (PLIP) not available

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

EDO.2: 8 residues within 4Å: Chain A: W.193, D.194, T.195, N.198, N.199, N.200, L.201, D.244 Ligand excluded by PLIP EDO.3: 6 residues within 4Å: Chain A: F.95, P.96, N.97, T.98, E.132, R.135 Ligand excluded by PLIP EDO.4: 6 residues within 4Å: Chain A: C.35, Y.39, L.230, V.231, G.232, L.233 Ligand excluded by PLIP EDO.5: 2 residues within 4Å: Chain A: S.227 Ligands: EDO.7 Ligand excluded by PLIP EDO.6: 3 residues within 4Å: Chain A: S.11, Y.39 Ligands: EDO.7 Ligand excluded by PLIP EDO.7: 4 residues within 4Å: Chain A: T.9, T.251 Ligands: EDO.5, EDO.6 Ligand excluded by PLIP EDO.8: 3 residues within 4Å: Chain A: L.25, P.26, Y.53 Ligand excluded by PLIP EDO.9: 5 residues within 4Å: Chain A: R.30, G.31, S.34, E.234, L.236 Ligand excluded by PLIP EDO.10: 3 residues within 4Å: Chain A: Q.90, E.91, I.92 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain A: R.127, S.130, R.162, Q.164, E.165 Ligand excluded by PLIP EDO.12: 6 residues within 4Å: Chain A: R.84, K.86, S.110, L.111, G.112, G.113 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain A: L.172, P.173, V.176, F.177 Ligand excluded by PLIP EDO.14: 2 residues within 4Å: Chain A: Y.74, M.100 Ligand excluded by PLIP EDO.15: 4 residues within 4Å: Chain A: H.188, Q.226, S.227, L.228 Ligand excluded by PLIP EDO.16: 4 residues within 4Å: Chain A: Y.64, T.65, I.66, K.82 Ligand excluded by PLIP EDO.17: 3 residues within 4Å: Chain A: P.51, P.52, A.55 Ligand excluded by PLIP EDO.18: 3 residues within 4Å: Chain A: N.70, M.101, N.103 Ligand excluded by PLIP EDO.19: 4 residues within 4Å: Chain A: R.30, C.33, S.34, R.60 Ligand excluded by PLIP EDO.20: 7 residues within 4Å: Chain A: C.33, L.36, A.37, R.60, A.61, S.63, Y.64 Ligand excluded by PLIP EDO.21: 3 residues within 4Å: Chain A: F.182, L.183, G.184 Ligand excluded by PLIP EDO.22: 2 residues within 4Å: Chain A: Y.191, K.208 Ligand excluded by PLIP EDO.23: 6 residues within 4Å: Chain A: P.51, C.54, T.68, N.70, E.71, F.75 Ligand excluded by PLIP

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

ACT.24: 6 residues within 4Å: Chain A: T.65, L.80, K.82, V.85, K.86, F.87 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:T.65, A:L.80, A:F.87 Hydrogen bonds: A:T.65, A:F.87 Water bridges: A:G.83 ACT.25: 3 residues within 4Å: Chain A: T.65, I.67, F.87 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.65, A:F.87 ACT.26: 3 residues within 4Å: Chain A: R.162, D.163, H.209 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.163 Water bridges: A:Q.164, A:H.209, A:H.209 Salt bridges: A:H.209

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

6AH.27: 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 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.125, A:S.125 Water bridges: A:N.16

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
B

Tyrosyl-DNA phosphodiesterase 2

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