SMTL ID : 4gz0.5 (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.22, EDO.23 Protein-ligand interaction information (PLIP) not available

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

EDO.2: 5 residues within 4Å: Chain A: K.196, A.197, N.199, K.235 Ligands: EDO.4 Ligand excluded by PLIP EDO.3: 6 residues within 4Å: Chain A: T.65, L.80, K.81, K.82, V.85, F.87 Ligand excluded by PLIP EDO.4: 7 residues within 4Å: Chain A: A.197, L.233, F.241, W.246 Ligands: EDO.2, EDO.10, EDO.11 Ligand excluded by PLIP EDO.5: 8 residues within 4Å: Chain A: K.187, H.188, Q.190, Y.191, D.194, A.197, W.246 Ligands: EDO.11 Ligand excluded by PLIP EDO.6: 2 residues within 4Å: Chain A: A.55 Ligands: ACT.21 Ligand excluded by PLIP EDO.7: 1 residues within 4Å: Chain A: S.227 Ligand excluded by PLIP EDO.8: 3 residues within 4Å: Chain A: C.54, K.58, I.66 Ligand excluded by PLIP EDO.9: 5 residues within 4Å: Chain A: S.34, C.35, L.38 Ligands: ACT.19, ACT.20 Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain A: L.233, E.234, K.235 Ligands: EDO.4 Ligand excluded by PLIP EDO.11: 4 residues within 4Å: Chain A: A.197, L.230 Ligands: EDO.4, EDO.5 Ligand excluded by PLIP EDO.12: 5 residues within 4Å: Chain A: D.163, V.166, E.181, R.210, R.213 Ligand excluded by PLIP EDO.13: 3 residues within 4Å: Chain A: E.27, R.30, D.237 Ligand excluded by PLIP EDO.14: 1 residues within 4Å: Chain A: E.71 Ligand excluded by PLIP EDO.15: 2 residues within 4Å: Chain A: Y.39, D.229 Ligand excluded by PLIP EDO.16: 1 residues within 4Å: Chain A: K.58 Ligand excluded by PLIP EDO.17: 5 residues within 4Å: Chain A: D.163, W.180, Q.190, R.210, R.213 Ligand excluded by PLIP EDO.23: 2 residues within 4Å: Chain A: L.20 Ligands: DC-DC-DG-DA-DA-DT-DT-DC-DG.1 Ligand excluded by PLIP

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

ACT.18: 6 residues within 4Å: Chain A: F.95, P.96, N.97, E.132, R.135, T.139 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.95, A:N.97, A:N.97 ACT.19: 6 residues within 4Å: Chain A: R.30, G.31, S.34, E.234, L.236 Ligands: EDO.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.34, A:E.234 ACT.20: 7 residues within 4Å: Chain A: C.35, Y.39, V.231, G.232, L.233, E.234 Ligands: EDO.9 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.39, A:V.231 Hydrogen bonds: A:G.232, A:L.233, A:E.234 Water bridges: A:G.232 ACT.21: 5 residues within 4Å: Chain A: P.51, P.52, A.55, K.58 Ligands: EDO.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.51, A:A.55 Salt bridges: A:K.58

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

6AH.22: 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 1 PLIP interactions: 1 interactions with chain A 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
I

Tyrosyl-DNA phosphodiesterase 2

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