SMTL ID : 4gz0.6 (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, F.211, D.244, H.245 Ligands: 6AH.19 Protein-ligand interaction information (PLIP) not available

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

EDO.2: 7 residues within 4Å: Chain A: W.193, D.194, T.195, N.198, N.200, L.201, D.244 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:W.193, A:D.194, A:N.198, A:N.200, A:L.201 EDO.3: 2 residues within 4Å: Chain A: H.188, D.229 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.188 EDO.4: 3 residues within 4Å: Chain A: S.34, A.37, L.38 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.34 EDO.5: 4 residues within 4Å: Chain A: R.30, G.31, S.34, L.236 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.30 Water bridges: A:R.30, A:R.30, A:D.237 EDO.6: 2 residues within 4Å: Chain A: A.197 Ligands: EDO.9 No protein-ligand interaction detected (PLIP) EDO.7: 3 residues within 4Å: Chain A: S.11, Y.39, S.40 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.11 EDO.8: 5 residues within 4Å: Chain A: L.25, P.26, P.52, Y.53, Y.56 No protein-ligand interaction detected (PLIP) EDO.9: 7 residues within 4Å: Chain A: Q.190, Y.191, D.194, A.197, L.230, W.246 Ligands: EDO.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.188, A:Q.190, A:Y.191, A:D.194 EDO.10: 4 residues within 4Å: Chain A: Y.39, D.229, L.230 Ligands: EDO.13 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.39, A:L.230, A:L.230 EDO.11: 6 residues within 4Å: Chain A: T.195, K.196, I.203, P.204, A.205, A.206 4 PLIP interactions: 4 interactions with chain A Water bridges: A:T.195, A:T.195, A:K.196, A:I.203 EDO.12: 2 residues within 4Å: Chain A: Q.190, Y.191 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.190, A:Y.191 Water bridges: A:Y.191 EDO.13: 7 residues within 4Å: Chain A: C.35, Y.39, L.230, V.231, G.232, L.233 Ligands: EDO.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.230, A:G.232 EDO.14: 2 residues within 4Å: Chain A: G.22, C.23 3 PLIP interactions: 3 interactions with chain A Water bridges: A:G.22, A:G.22, A:N.24 EDO.15: 3 residues within 4Å: Chain A: R.127, R.162 Ligands: ACT.16 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.127, A:R.127, A:R.162

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

ACT.16: 4 residues within 4Å: Chain A: R.162, D.163, H.209 Ligands: EDO.15 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.163 Water bridges: A:R.210 Salt bridges: A:H.209 ACT.17: 4 residues within 4Å: Chain A: K.196, A.197, N.199, K.235 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.196 Salt bridges: A:K.235 ACT.18: 6 residues within 4Å: Chain A: F.95, P.96, N.97, E.132, R.135, T.139 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:F.95, A:N.97, A:N.97, A:T.98 Salt bridges: A:R.135

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

6AH.19: 8 residues within 4Å: Chain A: L.20, E.48, Y.74, R.102, H.122, S.125, T.126 Ligands: DC-DC-DG-DA-DA-DT-DT-DC-DG.1 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.20 Hydrogen bonds: 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
K

Tyrosyl-DNA phosphodiesterase 2

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