Ligands, dictionary and refinement Garib N Murshudov York Structural Biology Laboratory University of York

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

1. Introduction
2. Dictionary of ligands
3. Sources of dictionary and idealised coordinates
4. Tools for ligand description in ccp4
5. How to use dictionary in refinement (REFMAC)
6. Conclusions

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The need for prior chemical knowledge

• Refinement
• Atomic model description

Graphics Simulations ..
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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
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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

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General category
data_comp_listloop__chem_comp.id_chem_comp.thre
e_letter_code_chem_comp.name_chem_comp.group_ch
em_comp.number_atoms_all_chem_comp.number_atoms_n
h_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
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Atom category
loop__chem_comp_atom.comp_id_chem_comp_atom.atom
_id_chem_comp_atom.type_symbol_chem_comp_atom.ty
pe_energy_chem_comp_atom.partial_charge_chem_com
p_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 . .
. . .
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Bond category
loop__chem_comp_bond.comp_id_chem_comp_bond.atom
_id_1_chem_comp_bond.atom_id_2_chem_comp_bond.ty
pe_chem_comp_bond.value_dist_chem_comp_bond.valu
e_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
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Angle category
loop__chem_comp_angle.comp_id_chem_comp_angle.at
om_id_1_chem_comp_angle.atom_id_2_chem_comp_angl
e.atom_id_3_chem_comp_angle.value_angle_chem_com
p_angle.value_angle_esd GLC-b-D H1 C1
O1 109.470 3.000 GLC-b-D O1 C1 C2
109.470 3.000. . . . . .
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Torsion angles category
loop__chem_comp_tor.comp_id_chem_comp_tor.id_ch
em_comp_tor.atom_id_1_chem_comp_tor.atom_id_2_ch
em_comp_tor.atom_id_3_chem_comp_tor.atom_id_4_ch
em_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
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Chirality category
1.Tetrahedral chirality
Usually on C or N with sp3 hybridisation
2.Non-tetrahedral chirality
Usually for metal coordination
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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.at
om_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

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Metal chirality
Metal chirality is only used to create
coordinates loop__chem_comp_chir.comp_id_chem_co
mp_chir.id_chem_comp_chir.atom_id_centre_chem_co
mp_chir.atom_id_1_chem_comp_chir.atom_id_2. . .
. _chem_comp_chir.atom_id_8_chem_comp_chir.volum
e_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
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Example metal chirality (OC7)
OC7 chir_01 CA O5 O7 O1 O4 O2 O3 O6 . cross5
O1
O4
O6
O5
O7
CA
O2
O3
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Plane category
loop__chem_comp_plane_atom.comp_id_chem_comp_pla
ne_atom.plane_id_chem_comp_plane_atom.atom_id_ch
em_comp_plane_atom.dist_esd PHE plan
CB 0.020 PHE plan CG
0.020 PHE plan CD1 0.020 . .
. . .
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Example of a modification
Modification formalism allows to change a monomer
Modification describes in details the result of
chemical reaction
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Modification general category
data_mod_listloop__chem_mod.id_chem_mod.name_c
hem_mod.comp_id_chem_mod.group_id. . . . . .
O1MET O1_metyl_of_sugar . pyranose
group_id means only for sugars
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Modification atom category
loop__chem_mod_atom.mod_id_chem_mod_atom.functio
n_chem_mod_atom.atom_id_chem_mod_atom.new_atom_i
d_chem_mod_atom.new_type_symbol_chem_mod_atom.ne
w_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
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Modification bond category
loop__chem_mod_bond.mod_id_chem_mod_bond.functio
n_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
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Example of peptide link
Link formalism allows to join monomers
together Link describes in details the result of
chemical reaction
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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_lin
k.group_comp_2_chem_link.nameALPHA1-4 . DEL-HO4
pyranose . DEL-O1 pyranose glycosidic_bond_alp
ha1-4
mod_id _1 modification of first monomer before
the linkage mod_id_2 modification of second
monomer before the linkage
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Link bond category
loop__chem_link_bond.link_id_chem_link_bond.atom
_1_comp_id_chem_link_bond.atom_id_1_chem_link_bo
nd.atom_2_comp_id_chem_link_bond.atom_id_2_chem_
link_bond.type_chem_link_bond.value_dist_chem_li
nk_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
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Source of dictionary and coordinates

• MSDchem
• PRODRG
• RELIBASE
• CORINA
• QM or other energy minimsation programs
• CSD

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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
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MSDchem JME
1) Draw substructure, write a smile file or
load SDF, MOL, mmCIF, 2) Search
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PRODRG server
JME
Load your file
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PRODRG JME
Draw your ligand, transfer to PRODRG window and
run
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PRODRG output
It can write out dictionaries for CNS REFMAC5,
SHELX and others
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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
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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
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Smile strings An example

• SMILE for ALA
• NC_at__at_H(C)C(O)O
• 3D representation

For description of smile http//www.daylight.com
/dayhtml_tutorials/languages/smiles/index.html
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Sketcher
Initial 2D sketch
After LIBCHECK and REFMAC
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Restraintsmonomer 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

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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
Modification ID
Standard name
Name in PDB file
MODRES GAL Y 2 GAL-b-D
RENAME
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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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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