SMTL ID : 3fsi.1

Crystal structure of a trypanocidal 4,4'-Bis(imidazolinylamino)diphenylamine bound to DNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

2 x DC- DT- DT- DA- DA- DT- DT- DC: 5'-D(*CP*TP*TP*AP*AP*TP*TP*C)-3'(Non-covalent)

DC-DT-DT-DA-DA-DT-DT-DC.1: 14 residues within 4Å: Chain A: P.77, V.78, R.93 Ligands: DG-DA-DA-DT-DT-DA-DA-DG.2, DG-DA-DA-DT-DT-DA-DA-DG.2, DG-DA-DA-DT-DT-DA-DA-DG.2, DG-DA-DA-DT-DT-DA-DA-DG.2, DG-DA-DA-DT-DT-DA-DA-DG.2, DG-DA-DA-DT-DT-DA-DA-DG.2, DG-DA-DA-DT-DT-DA-DA-DG.2, DG-DA-DA-DT-DT-DA-DA-DG.2, MWB.8, DC-DT-DT-DA-DA-DT-DT-DC.9, DG-DA-DA-DT-DT-DA-DA-DG.10 Protein-ligand interaction information (PLIP) not available DC-DT-DT-DA-DA-DT-DT-DC.9: 14 residues within 4Å: Chain B: P.77, V.78, R.93 Ligands: DC-DT-DT-DA-DA-DT-DT-DC.1, DG-DA-DA-DT-DT-DA-DA-DG.2, DG-DA-DA-DT-DT-DA-DA-DG.10, DG-DA-DA-DT-DT-DA-DA-DG.10, DG-DA-DA-DT-DT-DA-DA-DG.10, DG-DA-DA-DT-DT-DA-DA-DG.10, DG-DA-DA-DT-DT-DA-DA-DG.10, DG-DA-DA-DT-DT-DA-DA-DG.10, DG-DA-DA-DT-DT-DA-DA-DG.10, DG-DA-DA-DT-DT-DA-DA-DG.10, MWB.16 Protein-ligand interaction information (PLIP) not available

2 x DG- DA- DA- DT- DT- DA- DA- DG: 5'-D(P*GP*AP*AP*TP*TP*AP*AP*G)-3'(Non-covalent)

DG-DA-DA-DT-DT-DA-DA-DG.2: 18 residues within 4Å: Chain A: L.76, Q.90, D.91, L.92, R.93, N.96, G.168 Ligands: DC-DT-DT-DA-DA-DT-DT-DC.1, DC-DT-DT-DA-DA-DT-DT-DC.1, DC-DT-DT-DA-DA-DT-DT-DC.1, DC-DT-DT-DA-DA-DT-DT-DC.1, DC-DT-DT-DA-DA-DT-DT-DC.1, DC-DT-DT-DA-DA-DT-DT-DC.1, DC-DT-DT-DA-DA-DT-DT-DC.1, DC-DT-DT-DA-DA-DT-DT-DC.1, MWB.8, DC-DT-DT-DA-DA-DT-DT-DC.9, DG-DA-DA-DT-DT-DA-DA-DG.10 Protein-ligand interaction information (PLIP) not available DG-DA-DA-DT-DT-DA-DA-DG.10: 18 residues within 4Å: Chain B: L.76, Q.90, D.91, L.92, R.93, N.96, G.168 Ligands: DC-DT-DT-DA-DA-DT-DT-DC.1, DG-DA-DA-DT-DT-DA-DA-DG.2, DC-DT-DT-DA-DA-DT-DT-DC.9, DC-DT-DT-DA-DA-DT-DT-DC.9, DC-DT-DT-DA-DA-DT-DT-DC.9, DC-DT-DT-DA-DA-DT-DT-DC.9, DC-DT-DT-DA-DA-DT-DT-DC.9, DC-DT-DT-DA-DA-DT-DT-DC.9, DC-DT-DT-DA-DA-DT-DT-DC.9, DC-DT-DT-DA-DA-DT-DT-DC.9, MWB.16 Protein-ligand interaction information (PLIP) not available

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

ACT.3: 3 residues within 4Å: Chain A: Q.68, S.69, P.70 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.70 ACT.4: 5 residues within 4Å: Chain A: D.130, A.131, F.132, F.133, Q.167 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.133, A:Q.167 Hydrogen bonds: A:D.130, A:F.132, A:F.133 ACT.5: 4 residues within 4Å: Chain A: I.102, P.104, K.170, T.174 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:P.104 Hydrogen bonds: A:T.174 Water bridges: A:D.101, A:I.102, A:K.170, A:T.174 ACT.6: 6 residues within 4Å: Chain A: Q.40, M.43, R.48, E.148, W.149, R.150 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Q.40 Salt bridges: A:R.48 ACT.7: 4 residues within 4Å: Chain A: T.1, W.2, F.6, R.218 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.2 Salt bridges: A:R.218 ACT.11: 3 residues within 4Å: Chain B: Q.68, S.69, P.70 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:P.70 ACT.12: 5 residues within 4Å: Chain B: D.130, A.131, F.132, F.133, Q.167 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.133, B:Q.167 Hydrogen bonds: B:D.130, B:F.132, B:F.133 ACT.13: 4 residues within 4Å: Chain B: I.102, P.104, K.170, T.174 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:P.104 Hydrogen bonds: B:T.174 Water bridges: B:D.101, B:I.102, B:K.170, B:T.174 ACT.14: 6 residues within 4Å: Chain B: Q.40, M.43, R.48, E.148, W.149, R.150 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Q.40 Salt bridges: B:R.48 ACT.15: 4 residues within 4Å: Chain B: T.1, W.2, F.6, R.218 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:W.2 Salt bridges: B:R.218

2 x MWB: N1-(4,5-dihydro-1H-imidazol-2-yl)-N4-(4-((4,5-dihydro-1H-imidazol-2-yl)amino)phenyl)benzene-1,4-diamine(Non-functional Binders)

MWB.8: 10 residues within 4Å: Ligands: DC-DT-DT-DA-DA-DT-DT-DC.1, DC-DT-DT-DA-DA-DT-DT-DC.1, DC-DT-DT-DA-DA-DT-DT-DC.1, DC-DT-DT-DA-DA-DT-DT-DC.1, DC-DT-DT-DA-DA-DT-DT-DC.1, DG-DA-DA-DT-DT-DA-DA-DG.2, DG-DA-DA-DT-DT-DA-DA-DG.2, DG-DA-DA-DT-DT-DA-DA-DG.2, DG-DA-DA-DT-DT-DA-DA-DG.2, DG-DA-DA-DT-DT-DA-DA-DG.2 No protein-ligand interaction detected (PLIP) MWB.16: 10 residues within 4Å: Ligands: DC-DT-DT-DA-DA-DT-DT-DC.9, DC-DT-DT-DA-DA-DT-DT-DC.9, DC-DT-DT-DA-DA-DT-DT-DC.9, DC-DT-DT-DA-DA-DT-DT-DC.9, DC-DT-DT-DA-DA-DT-DT-DC.9, DG-DA-DA-DT-DT-DA-DA-DG.10, DG-DA-DA-DT-DT-DA-DA-DG.10, DG-DA-DA-DT-DT-DA-DA-DG.10, DG-DA-DA-DT-DT-DA-DA-DG.10, DG-DA-DA-DT-DT-DA-DA-DG.10 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Glass, L.S. et al., Crystal structure of a trypanocidal 4,4'-bis(imidazolinylamino)diphenylamine bound to DNA. Biochemistry (2009)

Release Date

2009-05-19

Peptides

Reverse transcriptase domain: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Reverse transcriptase domain

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