satarupa22/MacromolecularLigandDB huggingface dataset:
Structure of Thioesterase from DEBS with a thioesterase-specific antibody (PDB entry 6MLK)
Macromolecule: 6-deoxyerythronolide-B synthase EryA3, modules 5 and 6
Type: Protein, polypeptide(L)
Source organism: Saccharopolyspora erythraea
EC number: 2.3.1.94
Sequence length: 300 residues
Sequence: MASQLDSGTPAREASSALRDGYRQAGVSGRVRSYLDLLAGLSDFREHFDGSDGFSLDLVDMADGPGEVTVICCAGTAAISGPHEFTRLAGALRGIAPVRAVPQPGYEEGEPLPSSMAAVAAVQADAVIRTQGDKPFVVAGHSAGALMAYALATELLDRGHPPRGVVLIDVYPPGHQDAMNAWLEELTATLFDRETVRMDDTRLTALGAYDRLTGQWRPRETGLPTLLVSAGEPMGPWPDDSWKPTWPFEHDTVAVPGDHFTMVQEHADAIARHIDAWLGGGNSSSVDKLAAALEHHHHHH
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.45
R work: 0.1749
R free: 0.2352
Average B factor: 70.5827
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 295
Crystal growth procedure: 20% PEG3350, 15% Ethylene glycol, 0.2M Na2HPO4
Matthews coefficient: 2.7
Solvent content (%): 54.45
Ligand: CHLORIDE ION (CL)
Ligand formula: Cl
Ligand molecular weight: 35.453
Ligand SMILES: [Cl-]
Ligand InChI: InChI=1S/ClH/h1H/p-1
Release date: 2018-10-17
TTK kinase domain in complex with NTRC 0066-0 (PDB entry 5N87)
Macromolecule: Dual specificity protein kinase TTK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 313 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSMSVKGRIYSILKQIGSGGSSKVFQVLNEKKQIYAIKYVNLEEADNQTLDSYRNEIAYLNKLQQHSDKIIRLYDYEITDQYIYMVMECGNIDLNSWLKKKKSIDPWERKSYWKNMLEAVHTIHQHGIVHSDLKPANFLIVDGMLKLIDFGIANQMQPDTTSVVKDSQVGTVNYMPPEAIKDMSSSRENGKSKSKISPKSDVWSLGCILYYMTYGKTPFQQIINQISKLHAIIDPNHEIEFPDIPEKDLQDVLKCCLKRDPKQRISIPELLAHPYVQIQTHPVNQMAKGTTEE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.29
R work: 0.19782
R free: 0.23829
Average B factor: 67.76
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.3
Crystallization temperature (K): 293
Crystal growth procedure: 32 - 37% PEG400 (Acros, Geel, Belgium), 0.1 M Na/K phosphate pH 6.3 and 250 mM NaCl.
Matthews coefficient: 3.14
Solvent content (%): 60.82
Ligand: ~{N}-(2,6-diethylphenyl)-2-[[2-methoxy-4-(4-methylpiperazin-1-yl)phenyl]amino]-5,6-dihydropyrimido[4,5-e]indolizine-7-carboxamide (N66)
Ligand formula: C33 H39 N7 O2
Ligand molecular weight: 565.708
Ligand SMILES: CCc1cccc(c1NC(=O)c2ccn-3c2CCc4c3nc(nc4)Nc5ccc(cc5OC)N6CCN(CC6)C)CC
Ligand InChI: InChI=1S/C33H39N7O2/c1-5-22-8-7-9-23(6-2)30(22)36-32(41)26-14-15-40-28(26)13-10-24-21-34-33(37-31(24)40)35-27-12-11-25(20-29(27)42-4)39-18-16-38(3)17-19-39/h7-9,11-12,14-15,20-21H,5-6,10,13,16-19H2,1-4H3,(H,36,41)(H,34,35,37)
Release date: 2017-05-31
Crystal Structure of the R515Q missense variant of human PGM1 (PDB entry 5VIN)
Macromolecule: Phosphoglucomutase-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.4.2.2
Sequence length: 585 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSNMVKIVTVKTQAYQDQKPGTSGLRKRVKVFQSSANYAENFIQSIISTVEPAQRQEATLVVGGDGRFYMKEAIQLIARIAAANGIGRLVIGQNGILSTPAVSCIIRKIKAIGGIILTASHNPGGPNGDFGIKFNISNGGPAPEAITDKIFQISKTIEEYAVCPDLKVDLGVLGKQQFDLENKFKPFTVEIVDSVEAYATMLRSIFDFSALKELLSGPNRLKIRIDAMHGVVGPYVKKILCEELGAPANSAVNCVPLEDFGGHHPDPNLTYAADLVETMKSGEHDFGAAFDGDGDRNMILGKHGFFVNPSDSVAVIAANIFSIPYFQQTGVRGFARSMPTSGALDRVASATKIALYETPTGWKFFGNLMDASKLSLCGEESFGTGSDHIREKDGLWAVLAWLSILATRKQSVEDILKDHWQKYGRNFFTRYDYEEVEAEGANKMMKDLEALMFDRSFVGKQFSANDKVYTVEKADNFEYSDPVDGSISRNQGLRLIFTDGSRIVFRLSGTGSAGATIQLYIDSYEKDVAKINQDPQVMLAPLISIALKVSQLQERTGRTAPTVIT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.60004291837
R work: 0.238582434806
R free: 0.295418439253
Average B factor: 71.2698705059
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.01 M Cobalt (II) chloride hexahydrate, O.1 M MES monohydrate pH 6.5, Ammonium Sulfate 1.8-2.1M
Matthews coefficient: 3.06
Solvent content (%): 59.82
Ligand: GLYCEROL (GOL)
Ligand formula: C3 H8 O3
Ligand molecular weight: 92.094
Ligand SMILES: C(C(CO)O)O
Ligand InChI: InChI=1S/C3H8O3/c4-1-3(6)2-5/h3-6H,1-2H2
Release date: 2018-06-27
Structure of a protein-modified aptamer complex (PDB entry 7MK1)
Macromolecule: Antiviral innate immune response receptor RIG-I
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.4.13
Sequence length: 125 residues
Sequence: PDKENKKLLCRKCKALACYTADVRVIEECHYTVLGDAFKECFVSRPHPKPKQFSSFEKRAKIFCARQNCSHDWGIHVKYKTFEIPVIKIESFVVEDIATGVQTLYSKWKDFHFEKIPFDPAEMSK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.1884
R free: 0.2196
Average B factor: 47.59
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 285.15
Crystal growth procedure: 30% PEG3350, 0.01 M Na acetate pH 4.8
Matthews coefficient: 2.45
Solvent content (%): 49.8
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2021-11-03
CRYSTAL STRUCTURE OF DLK IN COMPLEX WITH COMPOUND 19 (PDB entry 8OUS)
Macromolecule: Mitogen-activated protein kinase kinase kinase 12
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.25
Sequence length: 300 residues
Sequence: MGSEDLWEVPFEEILDLQWVGSGAQGAVFLGRFHGEEVAVKKVRDLKETDIKHLRKLKHPNIITFKGVCTQAPCYCILMEFCAQGQLYEVLRAGRPVTPSLLVDWSMGIAGGMNYLHLHKIIHRDLKSPNMLITYDDVVKISDFGTSKELSDKSTKMSFAGTVAWMAPEVIRNEPVSEKVDIWSFGVVLWELLTGEIPYKDVDSSAIIWGVGSNSLHLPVPSSCPDGFKILLRQCWNSKPRNRPSFRQILLHLDIASADVLSTPQETYFKSQAEWREEVKLHFEKIKSEGTGNSHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.17941
R free: 0.2517
Average B factor: 33.94
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.7
Crystallization temperature (K): 291
Crystal growth procedure: 20% PEG 3350, 0.2 M magnesium acetate, and 0.1 M HEPES/NaOH pH 7.5-7.9
Matthews coefficient: 2.07
Solvent content (%): 40.44
Ligand: (1S)-1-[4-[6-azanyl-5-(trifluoromethyloxy)pyridin-3-yl]-1-(3-morpholin-4-yl-1-bicyclo[1.1.1]pentanyl)imidazol-2-yl]-2-methyl-propan-1-ol (W3I)
Ligand formula: C22 H28 F3 N5 O3
Ligand molecular weight: 467.485
Ligand SMILES: CC(C)C(c1nc(cn1C23CC(C2)(C3)N4CCOCC4)c5cc(c(nc5)N)OC(F)(F)F)O
Ligand InChI: InChI=1S/C22H28F3N5O3/c1-13(2)17(31)19-28-15(14-7-16(18(26)27-8-14)33-22(23,24)25)9-30(19)21-10-20(11-21,12-21)29-3-5-32-6-4-29/h7-9,13,17,31H,3-6,10-12H2,1-2H3,(H2,26,27)/t17-,20-,21+/m0/s1
Release date: 2023-07-26
Multiconformer synchrotron model of CypA at 100 K (PDB entry 4YUG)
Macromolecule: Peptidyl-prolyl cis-trans isomerase A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 165 residues
Sequence: MVNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFGSRNGKTSKKITIADCGQLE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.48
R work: 0.1327
R free: 0.1833
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291
Crystal growth procedure: Crystals were grown by mixing equal volumes of well solution (100 mM HEPES pH 7.5, 23% PEG 3350, 5 mM TCEP) and protein (60 mg/mL in 20 mM HEPES pH 7.5, 100 mM NaCl, 0.5 mM TCEP) in the hanging-drop format.
Matthews coefficient: 2.68
Solvent content (%): 54.04
Release date: 2015-10-14
CRYSTAL STRUCTURE OF HUMAN MONOGLYCERIDE LIPASE WITH LIGAND (PDB entry 7ZPG)
Macromolecule: Monoglyceride lipase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.1.23
Sequence length: 323 residues
Sequence: MGSSHHHHHHSSGENLYFQGMPEESSPRRTPQSIPYQDLPHLVNADGQYLFCRYWAPTGTPKALIFVSHGAGEHSGRYEELARMLMGLDLLVFAHDHVGHGQSEGERMVVSDFHVFVRDVLQHVDSMQKDYPGLPVFLLGHSMGGAIAILTAAERPGHFAGMVLISPLVLANPESATTFKVLAAKVLNSVLPNLSSGPIDSSVLSRNKTEVDIYNSDPLICRAGLKVCFGIQLLNAVSRVERALPKLTVPFLLLQGSADRLCDSKGAYLLMELAKSQDKTLKIYEGAYHVLHKELPEVTNSVFHEINMWVSQRTATAGTASPP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.16
R work: 0.1765
R free: 0.1845
Average B factor: 20.23
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 294
Crystal growth procedure: 0.1 M MES 6.5 pH
10 %w/v PEG MME 5K
12 %v/v iso-propanol
Matthews coefficient: 2.78
Solvent content (%): 55.73
Ligand: [(7R,9aR)-7-(4-chlorophenyl)-1,3,4,6,7,8,9,9a-octahydropyrido[1,2-a]pyrazin-2-yl]-(2-bromanyl-3-methoxy-phenyl)methanone (JQX)
Ligand formula: C22 H24 Br Cl N2 O2
Ligand molecular weight: 463.795
Ligand SMILES: COc1cccc(c1Br)C(=O)N2CCN3CC(CCC3C2)c4ccc(cc4)Cl
Ligand InChI: InChI=1S/C22H24BrClN2O2/c1-28-20-4-2-3-19(21(20)23)22(27)26-12-11-25-13-16(7-10-18(25)14-26)15-5-8-17(24)9-6-15/h2-6,8-9,16,18H,7,10-14H2,1H3/t16-,18+/m0/s1
Release date: 2022-09-21
Crystal structure of human GAA (PDB entry 5KZX)
Macromolecule: Lysosomal alpha-glucosidase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.1.20
Sequence length: 874 residues
Sequence: PTQCDVPPNSRFDCAPDKAITQEQCEARGCCYIPAKQGLQGAQMGQPWCFFPPSYPSYKLENLSSSEMGYTATLTRTTPTFFPKDILTLRLDVMMETENRLHFTIKDPANRRYEVPLETPHVHSRAPSPLYSVEFSEEPFGVIVHRQLDGRVLLNTTVAPLFFADQFLQLSTSLPSQYITGLAEHLSPLMLSTSWTRITLWNRDLAPTPGANLYGSHPFYLALEDGGSAHGVFLLNSNAMDVVLQPSPALSWRSTGGILDVYIFLGPEPKSVVQQYLDVVGYPFMPPYWGLGFHLCRWGYSSTAITRQVVENMTRAHFPLDVQWNDLDYMDSRRDFTFNKDGFRDFPAMVQELHQGGRRYMMIVDPAISSSGPAGSYRPYDEGLRRGVFITNETGQPLIGKVWPGSTAFPDFTNPTALAWWEDMVAEFHDQVPFDGMWIDMNEPSNFIRGSEDGCPNNELENPPYVPGVVGGTLQAATICASSHQFLSTHYNLHNLYGLTEAIASHRALVKARGTRPFVISRSTFAGHGRYAGHWTGDVWSSWEQLASSVPEILQFNLLGVPLVGADVCGFLGNTSEELCVRWTQLGAFYPFMRNHNSLLSLPQEPYSFSEPAQQAMRKALTLRYALLPHLYTLFHQAHVAGETVARPLFLEFPKDSSTWTVDHQLLWGEALLITPVLQAGKAEVTGYFPLGTWYDLQTVPIEALGSLPPPPAAPREPAIHSEGQWVTLPAPLDTINVHLRAGYIIPLQGPGLTTTESRQQPMALAVALTKGGEARGELFWDDGESLEVLERGAYTQVIFLARNNTIVNELVRVTSEGAGLQLQKVTVLGVATAPQQVLSNGVPVSNFTYSPDTKVLDICVSLLMGEQFLVSWC
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.154
R free: 0.185
Average B factor: 25.23
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 sodium HEPES, 2% (v/v) PEG 400, 2M ammonium sulfate
Matthews coefficient: 3.38
Solvent content (%): 63.57
Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose (NAG)
Ligand formula: C8 H15 N O6
Ligand molecular weight: 221.208
Ligand SMILES: CC(=O)NC1C(C(C(OC1O)CO)O)O
Ligand InChI: InChI=1S/C8H15NO6/c1-3(11)9-5-7(13)6(12)4(2-10)15-8(5)14/h4-8,10,12-14H,2H2,1H3,(H,9,11)/t4-,5-,6-,7-,8-/m1/s1
Release date: 2017-07-26
Human MMP12 in complex with 3-(5-(1,2-dithiolan-3-yl)pentanamido)propane-1-sulfonate (PDB entry 5N5J)
Macromolecule: Macrophage metalloelastase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.24.65
Sequence length: 158 residues
Sequence: GPVWRKHYITYRINNYTPDMNREDVDYAIRKAFQVWSNVTPLKFSKINTGMADILVVFARGAHGDDHAFDGKGGILAHAFGPGSGIGGDAHFDEDEFWTTHSGGTNLFLTAVHEIGHSLGLGHSSDPKAVMFPTYKYVDINTFRLSADDIRGIQSLYG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.12545
R free: 0.19533
Average B factor: 15.609
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M Tris-HCl, 20% PEG 6000
Matthews coefficient: 2.16
Solvent content (%): 42.96
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2017-11-01
PanDDA analysis group deposition -- Crystal Structure of Kalirin/Rac1 in complex with MolPort-009-565-301 (PDB entry 5QQL)
Macromolecule: Ras-related C3 botulinum toxin substrate 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 178 residues
Sequence: SMQAIKCVVVGDGAVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPVNLGLWDTAGQEDYDRLRPLSYPQTDVFLICFSLVSPASFENVRAKWYPEVRHHCPNTPIILVGTKLDLRDDKDTIEKLKEKKLTPITYPQGLAMAKEIGAVKYLECSALTQRGLKTVFDEAIRAVL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.25
R work: 0.1911
R free: 0.2702
Average B factor: 54.901
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 293.15
Crystal growth procedure: 0.1M bis-tris pH 5.5 24% PEG 3350
Matthews coefficient: 2.33
Solvent content (%): 47.12
Ligand: 1,2-ETHANEDIOL (EDO)
Ligand formula: C2 H6 O2
Ligand molecular weight: 62.068
Ligand SMILES: C(CO)O
Ligand InChI: InChI=1S/C2H6O2/c3-1-2-4/h3-4H,1-2H2
Release date: 2019-12-18
Human Cyclophilin D in complex with fragment (PDB entry 6R9U)
Macromolecule: Peptidyl-prolyl cis-trans isomerase F, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 164 residues
Sequence: GNPLVYLDVDANGKPLGRVVLELKADVVPKTAENFRALCTGEKGFGYKGSTFHRVIPSFMCQAGDFTNHNGTGGKSIYGSRFPDENFTLKHVGPGVLSMANAGPNTNGSQFFICTIKTDWLDGKHVVFGHVIEGMDVVKKIESFGSKSGRTSKKIVITDCGQLS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.26
R work: 0.149
R free: 0.172
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.2
Crystallization temperature (K): 298
Crystal growth procedure: 50 mM potassium phosphate
Matthews coefficient: 2.63
Solvent content (%): 53.32
Ligand: 14-ethyl-4,6-dioxa-10,14-diazatricyclo[7.6.0.0^{3,7}]pentadeca-1(9),2,7-trien-13-one (JVQ)
Ligand formula: C13 H16 N2 O3
Ligand molecular weight: 248.278
Ligand SMILES: CCN1Cc2cc3c(cc2NCCC1=O)OCO3
Ligand InChI: InChI=1S/C13H16N2O3/c1-2-15-7-9-5-11-12(18-8-17-11)6-10(9)14-4-3-13(15)16/h5-6,14H,2-4,7-8H2,1H3
Release date: 2019-11-27
The structure of human PDE12 residues 161-609 in complex with GSK3036342A (PDB entry 4Z2B)
Macromolecule: 2',5'-phosphodiesterase 12
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4
Sequence length: 455 residues
Sequence: YKVERNPPAFTELQLPRYIMAGFPVCPKLSLEFGDPASSLFRWYKEAKPGAAEPEVGVPSSLSPSSPSSSWTETDVEERVYTPSNADIGLRLKLHCTPGDGQRFGHSRELESVCVVEAGPGTCTFDHRHLYTKKVTEDALIRTVSYNILADTYAQTEFSRTVLYPYCAPYALELDYRQNLIQKELTGYNADVICLQEVDRAVFSDSLVPALEAFGLEGVFRIKQHEGLATFYRKSKFSLLSQHDISFYEALESDPLHKELLEKLVLYPSAQEKVLQRSSVLQVSVLQSTKDSSKRICVANTHLYWHPKGGYIRLIQMAVALAHIRHVSCDLYPGIPVIFCGDFNSTPSTGMYHFVINGSIPEDHEDWASNGEEERCNMSLTHFFKLKSACGEPAYTNYVGGFHGCLDYIFIDLNALEVEQVIPLPSHEEVTTHQALPSVSHPSDHIALVCDLKWK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.1815
R free: 0.2181
Average B factor: 21.79
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 295
Crystal growth procedure: 0.1M Tris Ph 8.5
15% Peg20000
25% Ethylene Glycol
Matthews coefficient: 2.32
Solvent content (%): 47.07
Ligand: SULFATE ION (SO4)
Ligand formula: O4 S
Ligand molecular weight: 96.063
Ligand SMILES: [O-]S(=O)(=O)[O-]
Ligand InChI: InChI=1S/H2O4S/c1-5(2,3)4/h(H2,1,2,3,4)/p-2
Release date: 2015-06-17
Crystal structure of human Naa50 in complex with a cofactor derived inhibitor (compound 1) (PDB entry 6WF3)
Macromolecule: N-alpha-acetyltransferase 50
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.258
Sequence length: 171 residues
Sequence: GSMKGSRIELGDVTPHNIKQLKRLNQVIFPVSYNDKFYKDVLEVGELAKLAYFNDIAVGAVCCRVDHSQNQKRLYIMTLGCLAPYRRLGIGTKMLNHVLNICEKDGTFDNIYLHVQISNESAIDFYRKFGFEIIETKKNYYKRIEPADAHVLQKNLKVPSGQNADVQKTDN
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.291
R work: 0.208
R free: 0.2434
Average B factor: 56.03
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 286.15
Crystal growth procedure: Naa50 apo protein (14.3 mg/ml) was incubated with compound 1 in a 1:3 molar ratio on ice for 60 min.  Reservoir solution containing 0.2 M ammonium sulfate and 30% (w/v) PEG 3K/4K was mixed 1:1 with protein/ligand complex
Matthews coefficient: 2.75
Solvent content (%): 55.26
Ligand: COENZYME A (COA)
Ligand formula: C21 H36 N7 O16 P3 S
Ligand molecular weight: 767.534
Ligand SMILES: CC(C)(COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)C(C(=O)NCCC(=O)NCCS)O
Ligand InChI: InChI=1S/C21H36N7O16P3S/c1-21(2,16(31)19(32)24-4-3-12(29)23-5-6-48)8-41-47(38,39)44-46(36,37)40-7-11-15(43-45(33,34)35)14(30)20(42-11)28-10-27-13-17(22)25-9-26-18(13)28/h9-11,14-16,20,30-31,48H,3-8H2,1-2H3,(H,23,29)(H,24,32)(H,36,37)(H,38,39)(H2,22,25,26)(H2,33,34,35)/t11-,14-,15-,16+,20-/m1/s1
Release date: 2020-07-01
Crystal structure of human Carbonic Anhydrase II in complex with 4-propoxybenzenesulfonamide (PDB entry 4RUY)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 260 residues
Sequence: MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.14
R work: 0.2013
R free: 0.2165
Average B factor: 12.1359
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 298
Crystal growth procedure: 1.6 M sodium citrate, 50 mM Tris-HCl, 3mM 4-propoxybenzenesulfonamide, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Matthews coefficient: 2.06
Solvent content (%): 40.29
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2015-04-22
Human cyclophilin A at 278K, Data set 5 (PDB entry 5KV3)
Macromolecule: Peptidyl-prolyl cis-trans isomerase A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 164 residues
Sequence: VNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFGSRNGKTSKKITIADCGQLE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.1553
R free: 0.2008
Average B factor: 22.0916
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 291
Crystal growth procedure: CRYSTALS WERE GROWN BY MIXING EQUAL VOLUMES OF WELL SOLUTION (100 MM HEPES PH 7.5, 23% PEG 3350, 5 MM TCEP) AND PROTEIN (60 MG/ML IN 20 MM HEPES PH 7.5, 100 MM NACL, 0.5 MM TCEP) IN THE HANGING-DROP FORMAT.
Matthews coefficient: 2.82
Solvent content (%): 56.32
Release date: 2016-08-10
Notum Inhibitor ARUK3006560 (PDB entry 8BSP)
Macromolecule: Palmitoleoyl-protein carboxylesterase NOTUM
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.1.98
Sequence length: 383 residues
Sequence: ETGSAQQLNEDLRLHLLLNTSVTCNDGSPAGYYLKESRGSRRWLLFLEGGWYCFNRENCDSRYDTMRRLMSSRDWPRTRTGTGILSSQPEENPYWWNANMVFIPYCSSDVWSGASSKSEKNEYAFMGALIIQEVVRELLGRGLSGAKVLLLAGSSAGGTGVLLNVDRVAEQLEKLGYPAIQVRGLADSGWFLDNKQYRHTDCVDTITCAPTEAIRRGIRYWNGVVPERCRRQFQEGEEWNCFFGYKVYPTLRSPVFVVQWLFDEAQLTVDNVHLTGQPVQEGLRLYIQNLGRELRHTLKDVPASFAPACLSHEIIIRSHWTDVQVKGTSLPRALHCWDRSLHDSHKASKTPLKGCPVHLVDSCPWPHCNPSCPTGTKHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.55
R work: 0.1877
R free: 0.2055
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 296
Crystal growth procedure: 1.5 M Ammonium Sulphate
0.1 M Sodium Citrate, pH4.2
Matthews coefficient: 1.93
Solvent content (%): 36.42
Ligand: SULFATE ION (SO4)
Ligand formula: O4 S
Ligand molecular weight: 96.063
Ligand SMILES: [O-]S(=O)(=O)[O-]
Ligand InChI: InChI=1S/H2O4S/c1-5(2,3)4/h(H2,1,2,3,4)/p-2
Release date: 2022-12-14
BACE1 in complex with a macrocyclic inhibitor (PDB entry 6NV9)
Macromolecule: Beta-secretase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.23.46
Sequence length: 390 residues
Sequence: GSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYNI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.13
R work: 0.1551
R free: 0.1902
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.2 M MgSO4
0.1 M Na citrate
14-20 % PEG 4000
Matthews coefficient: 3.2
Solvent content (%): 61.53
Ligand: (3S)-3-hydroxy-N-(2-methylpropyl)-N~2~-{[(4S)-17-[(methylsulfonyl)(propyl)amino]-2-oxo-3-azatricyclo[13.3.1.1~6,10~]icosa-1(19),6(20),7,9,15,17-hexaen-4-yl]methyl}-L-norleucinamide (L3M)
Ligand formula: C34 H52 N4 O5 S
Ligand molecular weight: 628.865
Ligand SMILES: CCCC(C(C(=O)NCC(C)C)NCC1Cc2cccc(c2)CCCCc3cc(cc(c3)N(CCC)S(=O)(=O)C)C(=O)N1)O
Ligand InChI: InChI=1S/C34H52N4O5S/c1-6-11-31(39)32(34(41)36-22-24(3)4)35-23-29-19-26-15-10-14-25(17-26)12-8-9-13-27-18-28(33(40)37-29)21-30(20-27)38(16-7-2)44(5,42)43/h10,14-15,17-18,20-21,24,29,31-32,35,39H,6-9,11-13,16,19,22-23H2,1-5H3,(H,36,41)(H,37,40)/t29-,31-,32-/m0/s1
Release date: 2019-10-09
Ankyrin domain of SKD3 isoform 2 (PDB entry 8FDS)
Macromolecule: Caseinolytic peptidase B protein homolog
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1
Sequence length: 182 residues
Sequence: YSKSPSNKDAALLEAARANNMQEVSRLLSEGADVNAKHRLGWTALMVAAINRNNSVVQVLLAAGADPNLGDDFSSVYKTAKEQGIHSLEVLITREDDFNNRLNNRASFKGCTALHYAVLADDYRTVKELLDGGANPLQRNEMGHTPLDYAREGEVMKLLRTSEAKYQEKQRKRELEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.65
R work: 0.1991
R free: 0.2207
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 9
Crystallization temperature (K): 287
Crystal growth procedure: 4 M potassium formate, 0.1 M Bis-Tris propane, pH 9.0, 2% w/v PEG2000 MME
Matthews coefficient: 2.32
Solvent content (%): 47.05
Ligand: FORMIC ACID (FMT)
Ligand formula: C H2 O2
Ligand molecular weight: 46.025
Ligand SMILES: C(=O)O
Ligand InChI: InChI=1S/CH2O2/c2-1-3/h1H,(H,2,3)
Release date: 2023-04-19
Ternary complex of human DNA Polymerase Mu with 2-nt gapped DNA substrate and an incoming nonhydrolyzable dUMPNPP (PDB entry 4YD1)
Macromolecule: DNA-directed DNA/RNA polymerase mu
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 354 residues
Sequence: GSAAASPAWMPAYACQRPTPLTHHNTGLSEALEILAEAAGFEGSEGRLLTFCRAASVLKALPSPVTTLSQLQGLPHFGEHSSRVVQELLEHGVCEEVERVRRSERYQTMKLFTQIFGVGVKTADRWYREGLRTLDDLREQPQKLTQQQKAGLQHHQDLSTPVLRSDVDALQQVVEEAVGQALPGATVTLTGGFRRGKLQGHDVDFLITHPKEGQEAGLLPRVMCRLQDQGLILYHQHQHSCCESPTRLAQQSHMDAFERSFCIFRLPQPGSWKAVRVDLVVAPVSQFPFALLGWTGSKLFQRELRRFSRKEKGLWLNSHGLFDPEQKTFFQAASEEDIFRHLGLEYLPPEQRNA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.75
R work: 0.163
R free: 0.19
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 294
Crystal growth procedure: 0.1M Tris, 20% PEG8K, 0.2M MgCl2
Matthews coefficient: 2.68
Solvent content (%): 54.03
Ligand: MAGNESIUM ION (MG)
Ligand formula: Mg
Ligand molecular weight: 24.305
Ligand SMILES: [Mg+2]
Ligand InChI: InChI=1S/Mg/q+2
Release date: 2015-08-05