SMTL ID : 4gz0.4 (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: 21 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.16, EDO.17, EDO.18, EDO.19 Protein-ligand interaction information (PLIP) not available

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

EDO.2: 6 residues within 4Å: Chain A: F.95, P.96, N.97, T.98, E.132, R.135 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:F.95, A:N.97, A:N.97, A:T.98, A:R.135 EDO.3: 3 residues within 4Å: Chain A: E.181, F.182 Ligands: EDO.5 No protein-ligand interaction detected (PLIP) EDO.4: 3 residues within 4Å: Chain A: S.227, T.251 Ligands: EDO.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.227, A:T.251 Water bridges: A:S.227 EDO.5: 3 residues within 4Å: Chain A: G.184, K.185 Ligands: EDO.3 1 PLIP interactions: 1 interactions with chain A Water bridges: A:G.184 EDO.6: 7 residues within 4Å: Chain A: H.188, Q.190, Y.191, D.194, A.197, L.230, W.246 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.188, A:Y.191, A:D.194, A:D.194 EDO.7: 2 residues within 4Å: Ligands: EDO.4, EDO.8 No protein-ligand interaction detected (PLIP) EDO.8: 6 residues within 4Å: Chain A: S.11, Y.39, S.40, P.41, L.249 Ligands: EDO.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.11 EDO.9: 5 residues within 4Å: Chain A: E.91, N.108, C.117, K.143, A.147 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.91, A:K.143 EDO.10: 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.11: 3 residues within 4Å: Chain A: L.183, G.184, P.186 3 PLIP interactions: 3 interactions with chain A Water bridges: A:G.184, A:K.185, A:K.187 EDO.12: 5 residues within 4Å: Chain A: D.21, C.23, N.200, R.202, R.240 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.240 EDO.17: 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 No protein-ligand interaction detected (PLIP) EDO.18: 1 residues within 4Å: Ligands: DC-DC-DG-DA-DA-DT-DT-DC-DG.1 No protein-ligand interaction detected (PLIP) EDO.19: 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, 6AH.16 1 PLIP interactions: 1 interactions with chain A Water bridges: A:L.20

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

ACT.13: 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, A:D.163 Water bridges: A:R.210, A:R.213 Salt bridges: A:H.209 ACT.14: 3 residues within 4Å: Chain A: R.127, S.130, E.165 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:E.165 Hydrogen bonds: A:S.130, A:E.165 Salt bridges: A:R.127, A:R.162 ACT.15: 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

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

6AH.16: 6 residues within 4Å: Chain A: E.48, R.102, H.122, S.125 Ligands: DC-DC-DG-DA-DA-DT-DT-DC-DG.1, EDO.19 2 PLIP interactions: 2 interactions with chain A 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
G

Tyrosyl-DNA phosphodiesterase 2

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