Ligands, dictionary and refinement
Garib N MurshudovYork Structural Biology Laboratory
University of York
Outline
1. Introduction2. Dictionary of ligands3. Sources of dictionary and idealised coordinates4. Tools for ligand description in ccp45. How to use dictionary in refinement (REFMAC)6. Conclusions
The need for prior chemical knowledge
• Refinement• Atomic model description
GraphicsSimulations………..
Atomic model description
. . . . . .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 . . . . . .
Default pointers in PDB file
Pointer to link description
Pointer to monomer description
Pointer to atom description
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
atoms
bonds
angles
torsions
chiralities
planes
tree
list of monomers
bonds
angles
torsions
chiralities
planes
tree
list of links
atoms
bonds
angles
torsions
chiralities
planes
tree
list of modifications
types
bonds
angles
VDW
H-bonds
list ofatom types
dictionary
General categorydata_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-polymerLevel: C or M – complete or minimal description
Atom categoryloop__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 . . . . .
Bond categoryloop__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
Angle categoryloop__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. . . . . .
Torsion angles categoryloop_
_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. . . . . .
Period: number of energetic minima
1
2 3
4
Chirality category
1.Tetrahedral chirality
2.Non-tetrahedral chirality
Usually on C or N with sp3 hybridisation
Usually for metalcoordination
Chirality categoryloop__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 . . . . .
Sign: positive, negative, both, anomer
1 3C
+_
Metal chiralityMetal chirality is only used to create coordinatesloop__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 cross6
Where: 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
Plane categoryloop__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 . . . . .
Example of a modification
CH2OHH
NH3+
O
O O
P
O
O O
3-
CH2H
NH3+
O
O
O
PO
OO
2-
+
OH-
Modification formalism allows to change a monomer
Modification describes in details the result of chemical reaction
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
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
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
Example of peptide link
Link formalism allows to join monomers together
Link describes in details the result of chemical reaction
R2H
NH3+
O
OR1H
NH3+
O
N
H O
O
HR2
R1H
NH3+
O
O+
H2O
Link: general categorydata_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
Link: bond categoryloop__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 monomeratom_2_comp_id: means second monomer
Source of dictionary and coordinates
• MSDchem• PRODRG• RELIBASE• CORINA• QM or other energy minimsation programs• CSD
MSDchemYou can search by formula, substructure and others. Results can be
save as cif file and used by libcheck to create dictionary for refmac
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
Ways to create dictionary
1. From chemical structure
2. From Cartesian coordinates
Using SKETCHER: monomer is drawn specifyingatoms and bondsFrom SMILE strings, sdf file, mol2 file
Coordinates from CSDEnergetically optimised coordinatesMOL2 fileSDF file
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
Restraints:monomer linkage
1. Chain links (trans/cis, DNA/RNA, sugar links, gap)
2. Standard links (SS bridges, sugar-protein links)
3. Potential links4. Links between alternative conformations5. Symmetry links6. User links
Modifications and links in PDB file
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
MODRES GAL Y 2 GAL-b-D RENAME
Modification IDStandard nameName in PDB file
Link ID
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)
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