Go away glycerol!!

Thursday, 7 November 2019

Go away glycerol!!

Due to the nature of crystallisation additives are often found in PDB structures. These are generally unwelcome, especially if you want to extract ligands. In fact, I have heard only once someone talk excitedly about their crystallisation reagent in their structure, but only because they were trying to flog it off as an allosteric binding site. Generally, they are just annoying. Luckily you don't need reinvent the wheel as a list or two already exist!

A great list of crystallisation reagents and common natural cofactors can be found in Peter Curran's repo for the HotSpots algorithm (first written by Chris Radoux). All that will be left are likely going to be bona fide ligands.

This may not suit all purposes as this includes common but natural metabolites, such as ATP.  For the name to PDB route in Michelaɴɢʟo I wanted to remove the crystallisation reagents and be left with natural metabolites or cofactors, drugs and other ligands. Therefore for my purposes I fetched the name of the ligand from the HotSpots Heteroatom list and manually removed the ones I cared about:

('WAT', 'HOH',  # `TP3` water is rare, but ambiguous!
'LI', 'NA' , 'K', 'RB',  # group 1 cations
'BE', 'MG', 'CA', 'SR',  # earth metal cations
'F', 'CL', 'BR', 'I',  #halogens
'MN', 'FE', 'CO',  'NI', 'CU', 'ZN',  # top period transition metals
'3CO',  # cobalt (iii) ion
'BUQ',  # 4-hydroxy-2-butanone
#'NAG',  # n-acetyl-d-glucosamine
#'NAD',  # nicotinamide-adenine-dinucleotide
'CR',  # chromium ion
#'SF4',  # iron/sulfur cluster
'EOH',  # ethanol
'ZNO',  # zinc ion, 2 waters coordinated
'NAO',  # sodium ion, 1 water coordinated
'EOM',  # ethyloxymethoxyl
'EHN',  # ethane
#'NAP',  # nadp nicotinamide-adenine-dinucleotide phosphate
'CCN',  # acetonitrile
'NAW',  # sodium ion, 3 waters coordinated
'BR',  # bromide ion
'EGL',  # ethylene glycol
'NI2',  # nickel (ii) ion, 2 waters coordinated
#'GSH',  # glutathione
'NI1',  # nickel ion, 1 water coordinated
#'O2',  # oxygen molecule
'BA',  # barium ion
'RU',  # ruthenium ion
#'SAH',  # s-adenosyl-l-homocysteine
'GU7', # 2-amino-7-[2-(2-hydroxy-1-hydroxymethyl-ethylamino)-ethyl]-1,7-dihydro-purin-6-one
#'SAM',  # s-adenosylmethionine
'TAS',  # trihydroxyarsenite(iii)
'DCE',  # 1,2-dichloroethane
'2BM',  # dibromomethane
#'TP7',  # coenzyme b
'OF3',  # ferric ion, 1 water coordinated
'OF1',  # ferrous ion, 1 water coordinated
'RB',  # rubidium ion
'IOH',  # 2-propanol, isopropanol
'MW1',  # manganese ion, 1 water coordinated
'IOD',  # iodide ion
'C2O',  # cu-o-cu linkage
'BNZ',  # benzene
'TCN',  # tetracyanonickelate ion
'ARS',  # arsenic
'NH4',  # ammonium ion
'GD',  # gadolinium atom
#'PER',  # peroxide ion
'GA',  # gallium (iii) ion
#'TPP',  # thiamine diphosphate
'CHX',  # cyclohexane
#'CME',  # s,s-(2-hydroxyethyl)thiocysteine
#'THB',  # tetrahydrobiopterin
'IPA',  # isopropyl alcohol
'CD1',  # cadmium ion, 1 water coordinated
'OH',  # hydroxide ion
'SO4',  # sulfate ion
'DTT',  # 2,3-dihydroxy-1,4-dithiobutane
#'PQN',  # phylloquinone
'CYN',  # cyanide ion
#'PQQ',  # pyrroloquinoline quinone
'PYJ',  # phenylethane
#'PEO',  # hydrogen peroxide
'NA6',  # sodium ion, 6 waters coordinated
'MBR',  # tribromomethane
'NA5',  # sodium ion, 5 waters coordinated
'OS',  # osmium ion
'MAN',  # alpha-d-mannose
'CMO',  # carbon monoxide
'OCL',  # cobalt ion, 1 water coordinated
'DMF',  # dimethylformamide
'OCN',  # cobalt ion, 2 waters coordinated
'MO3',  # magnesium ion, 3 waters coordinated
'NGN',  # nitrogen
'ACT',  # acetate ion
'U1',  # uranium atom
'HDZ',  # nitrogen molecule
'MO5',  # magnesium ion, 5 waters coordinated
'MO4',  # magnesium ion, 4 waters coordinated
'VO4',  # vanadate ion
'DMS',  # dimethyl sulfoxide
'FUC',  # alpha-l-fucose
'PCL',  # platinum(ii) di-chloride
'CB5',  # cobalt bis(1,2-dicarbollide)
'EEE',  # ethyl acetate
'HG',  # mercury (ii) ion
'NO2',  # nitrite ion
#'CMP',  # adenosine-3',5'-cyclic-monophosphate
'PR',  # praseodymium ion
'BMA',  # beta-d-mannose
'IUM',  # uranyl (vi) ion
'PT',  # platinum (ii) ion
'ZN2',  # zinc ion on 3-fold crystal axis
#'TTP',  # thymidine-5'-triphosphate
'NO3',  # nitrate ion
'YT3',  # yttrium (iii) ion
#'TYS',  # o-sulfo-l-tyrosine
'PB',  # lead (ii) ion
'M2M',  # 1-methoxy-2-(2-methoxyethoxy)ethane
'ZO3',  # zinc ion, 3 waters coordinated
'PD',  # palladium ion
#'AMP',  # adenosine monophosphate
'PI',  # hydrogenphosphate ion
'MH3',  # manganese ion, 1 hydroxyl coordinated
'AF3',  # aluminum fluoride
'ZN',  # zinc ion
'MN3',  # manganese (iii) ion
'OXY',  # oxygen molecule
'NI',  # nickel (ii) ion
#'CSD',  # 3-sulfinoalanine
#'OX',  # bound oxygen
'PS5',  # pentasulfide-sulfur
'MN5',  # manganese ion, 5 waters coordinated
'MN6',  # manganese ion, 6 waters coordinated
'S',  # sulfur atom
'HOH',  # water
'W',  # tungsten ion
'SB',  # antimony (iii) ion
#'FOL',  # folic acid
'OXE',  # ortho-xylene
'PT4',  # platinum (iv) ion
'PBM',  # trimethyl lead ion
'O',  # oxygen atom
'MW2',  # manganese dihydrate ion
'MG',  # magnesium ion
'543',  # calcium ion, 6 waters plus ethanol coordinated
'MSM',  # (methylsulfanyl)methane
#'C5P',  # cytidine-5'-monophosphate
'ANL',  # aniline
'MTO',  # bound water
'NO',  # nitric oxide
'TBU',  # tertiary-butyl alcohol
'OPY',  # (3s)-4-oxo-4-piperidin-1-ylbutane-1,3-diamine
'PC4',  # tetrachloroplatinate(ii)
#'GU3',  # methyl 3-o-methyl-2,6-di-o-sulfo-alpha-d-glucopyranoside
#'GU2',  # 2,3-di-o-methyl-alpha-l-idopyranuronic acid
#'GU1',  # 2,3-di-o-methyl-beta-d-glucopyranuronic acid
'MOH',  # methanol
#'ANP',  # phosphoaminophosphonic acid-adenylate ester
#'GU6',  # 2,3,6-tri-o-sulfonato-alpha-d-glucopyranose
#'GU5',  # 2,3-di-o-methyl-6-o-sulfonato-alpha-d-glucopyranose
#'GU4',  # 2,3,4,6-tetra-o-sulfonato-alpha-d-glucopyranose
'AU',  # gold ion
'OC3',  # calcium ion, 3 waters coordinated
'BTN',  # biotin
'I42',  # hydroxy(dioxido)oxovanadium
'OC4',  # calcium ion, 4 waters coordinated
'OC7',  # calcium ion, 7 waters coordinated
'OC6',  # calcium ion, 6 waters coordinated
#'TMP',  # thymidine-5'-phosphate
'RE',  # rhenium
'GD3',  # gadolinium ion
#'CTP',  # cytidine-5'-triphosphate
'ACE',  # acetyl group
'3OF',  # hydrated fe (iii) ion, 2 waters coordinated
'ETZ',  # diethyl ether
'MM4',  # molybdenum (iv) oxide
'IN',  # indium (iii) ion
'ACN',  # acetone
'DOD',  # deuterated water
'AST',  # arsenite
#'COA',  # coenzyme a
'EU',  # europium ion
'DOX',  # dioxane
#'COB',  # co-methylcobalamin
#'B12',  # cobalamin
'REO',  # perrhenate
#'ATP',  # adenosine-5'-triphosphate
'CD3',  # cadmium ion, 3 waters coordinated
#'U10',  # ubiquinone-10
'ACY',  # acetic acid
'PEG',  # di(hydroxyethyl)ether
'YB',  # ytterbium (iii) ion
#'NDP',  # nadph dihydro-nicotinamide-adenine-dinucleotide phosphate
'NBZ',  # nitrobenzene
'ETI',  # iodoethane
'SER',  # serine
'C2C',  # cu-cl-cu linkage
'NA',  # sodium ion
'FMT',  # formic acid
'ASC',  # ascorbic acid
'AU3',  # gold 3+ ion
'FE2',  # fe (ii) ion
'LNK',  # pentane
'SEK',  # selenocyanate ion
'MO1',  # magnesium ion, 1 water coordinated
'EU3',  # europium (iii) ion
'1BO',  # 1-butanol
'AUC',  # gold (i) cyanide ion
'CLO',  # chloro group
'FE',  # fe (iii) ion
'DUM',  # dummy atoms
#'ADP',  # adenosine-5'-diphosphate
'OF2',  # 2 ferric ion, 1 bridging oxygen
'BEF',  # beryllium trifluoride ion
'FEL',  # hydrated fe
'BF4',  # beryllium tetrafluoride ion
'HEX',  # hexane
'CUZ',  # (mu-4-sulfido)-tetra-nuclear copper ion
#'NDG',  # 2-(acetylamino)-2-deoxy-a-d-glucopyranose
'XE',  # xenon
#'FMN',  # flavin mononucleotide
'YAN',  # 1,2-dichlorobenzene
'CUA',  # dinuclear copper ion
'V',  # vanadium ion
'CUO',  # cu2-o2 cluster
#'HEM',  # protoporphyrin ix containing fe
#'GMP',  # guanosine
'CU',  # copper (ii) ion
'MGF',  # trifluoromagnesate
#'GDP',  # guanosine-5'-diphosphate
'CFT',  # trifluoromethane
'SBT',  # 2-butanol
#'PLP',  # pyridoxal-5'-phosphate
'SR',  # strontium ion
'FU1',  # tetrahydrofuran
'EDN',  # ethane-1,2-diamine
'EDO',  # 1,2-ethanediol
'H2S',  # hydrosulfuric acid
'ND4',  # ammonium cation with d
'BRO',  # bromo group
'KR',  # krypton
'CS',  # cesium ion
'NME',  # methylamine
#'CDP',  # cytidine-5'-diphosphate
'HGI',  # mercury (ii) iodide
'SM',  # samarium (iii) ion
#'ALY',  # n(6)-acetyllysine
#'NMO',  # nitrogen monoxide
#'TDP',  # thiamin diphosphate
'SE',  # selenium atom
'HO',  # holmium atom
'3CN',  # 3-aminopropane
'AZI',  # azide ion
#'F42',  # coenzyme f420
'FLO',  # fluoro group
'6MO',  # molybdenum(vi) ion
'EMC',  # ethyl mercury ion
'Y1',  # yttrium ion
#'MO7', # bis(mu4-oxo)-bis(mu3-oxo)-octakis(mu2-oxo)-dodecaoxo-heptamolybdenum (vi)
'SE4',  # selenate ion
'BF2',  # beryllium difluoride
'CO',  # cobalt (ii) ion
#'NGD', # 3-(aminocarbonyl)-1-[(2r,3r,4s,5r)-5-({[(s)-{[(s)-{[(2r,3s,4r,5r)-5-(2-amino-6-oxo-1,6-dihydro-9h-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}methyl)-3,4-dihydroxytetrahydrofuran-2-yl]pyridinium
'2MO',  # molybdenum (iv)oxide
'202',  # bromic acid
'DIS',  # disordered solvent
'MBN',  # toluene
'LA',  # lanthanum (iii) ion
'PGO',  # s-1,2-propanediol
'CL',  # chloride ion
'HP6',  # heptane
'SO2',  # sulfur dioxide
'LI',  # lithium ion
#'PPS',  # 3'-phosphate-adenosine-5'-phosphate sulfate
#'TPO',  # phosphothreonine
'POL',  # n-propanol
#'GU0',  # 2,3,6-tri-o-sulfonato-alpha-l-galactopyranose
'SGM',  # monothioglycerol
'DTU',  # (2r,3s)-1,4-dimercaptobutane-2,3-diol
'MOO',  # molybdate ion
'TE',  # tellurium
'TB',  # terbium(iii) ion
'CA',  # calcium ion
#'FAD',  # flavin-adenine dinucleotide
'CNV',  # propanenitrile
'GOL',  # glycerol
'SCN',  # thiocyanate ion
'AG',  # silver ion
'PO4',  # phosphate ion
'IR',  # iridium ion
'DIO',  # 1,4-diethylene dioxide
'NH2',  # amino group
'8CL',  # chlorobenzene
'3NI',  # nickel (iii) ion
'IRI',  # iridium hexammine ion
#'UTP',  # uridine 5'-triphosphate
'AR',  # argon
#'N4M', # 5-formyltetrahydromethanopterin
'CE',  # cerium (iii) ion
'NH3',  # ammonia
'MN',  # manganese (ii) ion
'CNN',  # cyanamide
'HGC',  # methyl mercury ion
#'GU8',  # 2,3,6-tri-o-methyl-beta-d-glucopyranose
#'GTP',  # guanosine-5'-triphosphate
#'UDP',  # uridine-5'-diphosphate
'OC2',  # calcium ion, 2 waters coordinated
'ART',  # arsenate
'TFH',  # nitrogen of trifluoro-ethylhydrazine
'MCH',  # trichloromethane
'2NO',  # nitrogen dioxide
'6WO',  # oxo-tungsten(vi)
'CD5',  # cadmium ion, 5 waters coordinated
#'KCX',  # lysine nz-carboxylic acid
'E1H',  # ethanimine
'ARF',  # formamide
'TL',  # thallium (i) ion
'DXE',  # 1,2-dimethoxyethane
#'GU9',  # 2,3,6-tri-o-methyl-alpha-d-glucopyranose
'IDO',  # iodo group
'KO4',  # potassium ion, 4 waters coordinated
'NRU',  # ruthenium (iii) hexaamine ion
'4MO'  # molybdenum(iv) ion
)
One thing to note is that heavy metals often replace lighter ions to help solve the phasing problem. Therefore, stripping these could be incorrect. Instead they ought to be changed in both name and element to the correct one in the PDB/CIF file if they are legitimate. Likewise, in some cases glucose is a crystallisation reagent, other times it is the substrate. So for some cases there is not really a one size fits all, but a one size fits the vast majority of cases.

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