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Ligands, dictionary and refinement Garib N Murshudov York Structural Biology Laboratory University of York. Outline. Introduction Dictionary of ligands Sources of dictionary and idealised coordinates Tools for ligand description in ccp4 How to use dictionary in refinement (REFMAC)

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  1. Ligands, dictionary and refinementGarib N MurshudovYork Structural Biology LaboratoryUniversity of York

  2. Outline • Introduction • Dictionary of ligands • Sources of dictionary and idealised coordinates • Tools for ligand description in ccp4 • How to use dictionary in refinement (REFMAC) • Conclusions

  3. The need for prior chemical knowledge • Refinement • Atomic model description Graphics Simulations ………..

  4. Atomic model description Default pointers in PDB file . . . . . .ATOM 7 C LEU A 5 37.584 4.085 ATOM 8 O LEU A 5 36.548 3.447 ATOM 9 N ILE A 6 37.887 5.098 ATOM 10 CA ILE A 6 37.032 5.447 ATOM 11 CB ILE A 6 37.835 6.276 . . . . . . Pointer to link description Pointer to monomer description Pointer to atom description

  5. Refmac5 Dictionary • Describes all amino acids • All nucleic acids • Common sugars • Many organic and inorganic compounds • Links and modifications There are tools to deal with dictionary Dictionary format is mmCIF

  6. General category data_comp_listloop__chem_comp.id_chem_comp.three_letter_code_chem_comp.name_chem_comp.group_chem_comp.number_atoms_all_chem_comp.number_atoms_nh_chem_comp.desc_level. . . . . . . . . GLC-b-D GLC 'beta_D_glucose ' D-pyranose 24 12 . Group: peptide, DNA/RNA, pyranose, non-polymer Level: C or M – complete or minimal description

  7. Atom category loop__chem_comp_atom.comp_id_chem_comp_atom.atom_id_chem_comp_atom.type_symbol_chem_comp_atom.type_energy_chem_comp_atom.partial_charge_chem_comp_atom.x_chem_comp_atom.y_chem_comp_atom.z GLC-b-D C1 C CH1 0 0.0 0.0 0.0 GLC-b-D H1 H HCH1 0 0.522 -0.087 0.801 . . . . .

  8. Bond category loop__chem_comp_bond.comp_id_chem_comp_bond.atom_id_1_chem_comp_bond.atom_id_2_chem_comp_bond.type_chem_comp_bond.value_dist_chem_comp_bond.value_dist_esd GLC-b-D O1 C1 single 1.410 0.020 GLC-b-D C2 C1 single 1.524 0.020 . . . . . Type: single, double, triple, aromatic, metal

  9. Angle category loop__chem_comp_angle.comp_id_chem_comp_angle.atom_id_1_chem_comp_angle.atom_id_2_chem_comp_angle.atom_id_3_chem_comp_angle.value_angle_chem_comp_angle.value_angle_esd GLC-b-D H1 C1 O1 109.470 3.000 GLC-b-D O1 C1 C2 109.470 3.000. . . . . .

  10. Torsion angles category loop__chem_comp_tor.comp_id_chem_comp_tor.id_chem_comp_tor.atom_id_1_chem_comp_tor.atom_id_2_chem_comp_tor.atom_id_3_chem_comp_tor.atom_id_4_chem_comp_tor.value_angle_chem_comp_tor.value_angle_esd_chem_comp_tor.period GLC-b-D var_1 C1 C2 O2 HO2 0.000 20.000 1 GLC-b-D var_2 C1 C2 C3 C4 -50.095 20.000 3. . . . . . 1 4 2 3 Period: number of energetic minima

  11. Chirality category 1.Tetrahedral chirality Usually on C or N with sp3 hybridisation 2.Non-tetrahedral chirality Usually for metal coordination

  12. Chirality category loop__chem_comp_chir.comp_id_chem_comp_chir.id_chem_comp_chir.atom_id_centre_chem_comp_chir.atom_id_1_chem_comp_chir.atom_id_2_chem_comp_chir.atom_id_3_chem_comp_chir.volume_signGLC-b-D chir_01 C5 C4 O5 C6 positiveGLC-b-D chir_02 C4 C3 O4 C5 positive GLC-b-D chir_03 C3 C2 O3 C4 negative GLC-b-D chir_04 C2 C1 O2 C3 positive . . . . . 1 3 C _ Sign: positive, negative, both, anomer +

  13. Metal chirality is only used to create coordinates loop__chem_comp_chir.comp_id_chem_comp_chir.id_chem_comp_chir.atom_id_centre_chem_comp_chir.atom_id_1_chem_comp_chir.atom_id_2. . . . _chem_comp_chir.atom_id_8_chem_comp_chir.volume_signMONid chir_id Ac Ab Af A1 A2 A3 A4 A5 A6 cross6Where: Ac - chiral centre atom Ab - back atom,Af - forward atom A1,A2,...,AN - atoms in the same plane, N can be = 0,1,2,3,4,5,6 these atoms form the point group. crossN - cross chirality specification Metal chirality

  14. Example metal chirality (OC7) OC7 chir_01 CA O5 O7 O1 O4 O2 O3 O6 . cross5 O1 O4 O6 O5 O7 CA O3 O2

  15. Plane category loop__chem_comp_plane_atom.comp_id_chem_comp_plane_atom.plane_id_chem_comp_plane_atom.atom_id_chem_comp_plane_atom.dist_esd PHE plan CB 0.020 PHE plan CG 0.020 PHE plan CD1 0.020 . . . . .

  16. Example of a modification Modification formalism allows to change a monomer Modification describes in details the result of chemical reaction

  17. Modification: general category data_mod_listloop__chem_mod.id_chem_mod.name_chem_mod.comp_id_chem_mod.group_id. . . . . . O1MET O1_metyl_of_sugar . pyranose group_id: means only for sugars

  18. Modification: atom category loop__chem_mod_atom.mod_id_chem_mod_atom.function_chem_mod_atom.atom_id_chem_mod_atom.new_atom_id_chem_mod_atom.new_type_symbol_chem_mod_atom.new_type_energy_chem_mod_atom.new_partial_charge O1MET change O1 . . O2 0.000 O1MET delete HO1 . . . 0.000 O1MET add . CM C CH3 0.000 O1MET add . HM1 H HCH 0.000 . . . . . . function: only - change, delete or add

  19. Modification: bond category loop__chem_mod_bond.mod_id_chem_mod_bond.function_chem_mod_bond.atom_id_1_chem_mod_bond.atom_id_2_chem_mod_bond.new_type_chem_mod_bond.new_value_dist_chem_mod_bond.new_value_dist_esd O1MET add O1 CM single 1.420 0.020 O1MET add CM HM1 single 0.960 0.020 O1MET add CM HM2 single 0.960 0.020 O1MET add CM HM3 single 0.960 0.020

  20. Example of peptide link Link formalism allows to join monomers together Link describes in details the result of chemical reaction

  21. Link: general category data_link_listloop__chem_link.id_chem_link.comp_id_1_chem_link.mod_id_1_chem_link.group_comp_1_chem_link.comp_id_2_chem_link.mod_id_2_chem_link.group_comp_2_chem_link.nameALPHA1-4 . DEL-HO4 pyranose . DEL-O1 pyranose glycosidic_bond_alpha1-4 mod_id _1: modification of first monomer before the linkage mod_id_2 : modification of second monomer before the linkage

  22. Link: bond category loop__chem_link_bond.link_id_chem_link_bond.atom_1_comp_id_chem_link_bond.atom_id_1_chem_link_bond.atom_2_comp_id_chem_link_bond.atom_id_2_chem_link_bond.type_chem_link_bond.value_dist_chem_link_bond.value_dist_esd ALPHA1-4 1 O4 2 C1 single 1.439 0.020 atom_1_comp_id: means first monomer atom_2_comp_id: means second monomer

  23. Source of dictionary and coordinates • MSDchem • PRODRG • RELIBASE • CORINA • QM or other energy minimsation programs • CSD

  24. MSDchem You can search by formula, substructure and others. Results can be save as cif file and used by libcheck to create dictionary for refmac

  25. MSDchem: JME 1) Draw substructure, write a smile file or load SDF, MOL, mmCIF, 2) Search

  26. PRODRG server JME Load your file

  27. PRODRG: JME Draw your ligand, transfer to PRODRG window and run

  28. PRODRG output It can write out dictionaries for CNS REFMAC5, SHELX and others

  29. Tools in CCP4 LIBCHECK - creates the complete monomer description from minimal - creates coordinates from complete monomer description SKETCHER - graphical program that creates the minimal monomer description for LIBCHECK MAKECIF - creates restraints

  30. Ways to create dictionary 1. From chemical structure Using SKETCHER: monomer is drawn specifying atoms and bonds From SMILE strings, sdf file, mol2 file 2. From Cartesian coordinates Coordinates from CSD Energetically optimised coordinates MOL2 file SDF file

  31. Smile strings: An example SMILE for ALA: N[C@@H](C)C(=O)O 3D representation: For description of smile: http://www.daylight.com/dayhtml_tutorials/languages/smiles/index.html

  32. Sketcher Initial 2D sketch After LIBCHECK and REFMAC

  33. Restraints:monomer linkage • Chain links (trans/cis, DNA/RNA, sugar links, gap) • Standard links (SS bridges, sugar-protein links) • Potential links • Links between alternative conformations • Symmetry links • User links

  34. Modifications and links in PDB file Link ID SSBOND 1 CYS L 88 CYS L 23LINK SG CYS H 195 2.031 SG BCYS H 140 SSLINK TYR L 139 PRO L 140 PCISLINK GLY H 127 GLY H 133 gapLINK MAG Y 1 GAL Y 2 BETA1-4LINK O LEU B 61 NA NA X 6 LEU-NALINK OE1 GLU A 139 NA NA X 1 12555 symmetry Standard name Modification ID Name in PDB file MODRES GAL Y 2 GAL-b-D RENAME

  35. Conclusions • Ligand dictionaries should designed with care. Interpetation of chemistry may depend on that • Such resources as MSDchem, PRODRG can help to create an accurate dictionary • Links and modifications are important component for understanding protein chemistry • Unfortunately no automatic link generation programs available yet (we are working on that)

  36. Acknowledgments • Alexei Vagin – YSBL, York • Roberto Steiner – Kings coll. • Andrey Lebedev – YSBL, York • Liz Potterton – YSBL, York • Fei Long – YSBL, York • Wellcome Trust, BBSRC, BIOXHIT, CCP4 – money

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