satarupa22/MacromolecularLigandDB huggingface dataset:
Human OSGEP / LAGE3 / GON7 complex (PDB entry 6GWJ)
Macromolecule: EKC/KEOPS complex subunit LAGE3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 143 residues
Sequence: MRDADADAGGGADGGDGRGGHSCRGGVDTAAAPAGGAPPAHAPGPGRDAASAARGSRMRPHIFTLSVPFPTPLEAEIAHGSLAPDAEPHQRVVGKDLTVSGRILVVRWKAEDCRLLRISVINFLDQLSLVVRTMQRFGPPVSR
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.95
R work: 0.186
R free: 0.217
Average B factor: 54.83
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: of PEG 4000, 0.1 M Tris HCl pH 8.5 and 0.2 M Magnesium Chloride
Matthews coefficient: 2.25
Solvent content (%): 45.38
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: 2019-07-03
Caspase-8 specific unnatural amino acid peptides (PDB entry 4PS1)
Macromolecule: Caspase-8
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.22.61
Sequence length: 275 residues
Sequence: MSESQTLDKVYQMKSKPRGYCLIINNHNFAKAREKVPKLHSIRDRNGTHLDAGALTTTFEELHFEIKPHDDCTVEQIYEILKIYQLMDHSNMDCFICCILSHGDKGIIYGTDGQEAPIYELTSQFTGLKCPSLAGKPKVFFIQACQGDNYQKGIPVETDSEEQPYLEMDLSSPQTRYIPDEADFLLGMATVNNCVSYRNPAEGTWYIQSLCQSLRERCPRGDDILTILTEVNYEVSNKDDKKNMGKQMPQPTFTLRKKLVFPSDAAALEHHHHHH
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.731
R work: 0.1522
R free: 0.1846
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 295
Crystal growth procedure: 0.1 M Sodium citrate, pH 5.5, 36% PEG600, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Matthews coefficient: 2.33
Solvent content (%): 47.24
Ligand: 2,3-DIHYDROXY-1,4-DITHIOBUTANE (DTT)
Ligand formula: C4 H10 O2 S2
Ligand molecular weight: 154.251
Ligand SMILES: C(C(C(CS)O)O)S
Ligand InChI: InChI=1S/C4H10O2S2/c5-3(1-7)4(6)2-8/h3-8H,1-2H2/t3-,4-/m0/s1
Release date: 2015-01-21
STRUCTURE OF FULL LENGTH HUMAN AMPK (NON-PHOSPHORYLATED AT T-LOOP) IN COMPLEX WITH A SMALL MOLECULE ACTIVATOR, A BENZIMIDAZOLE DERIVATIVE (991) (PDB entry 5ISO)
Macromolecule: 5'-AMP-activated protein kinase catalytic subunit alpha-2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 552 residues
Sequence: MAEKQKHDGRVKIGHYVLGDTLGVGTFGKVKIGEHQLTGHKVAVKILNRQKIRSLDVVGKIKREIQNLKLFRHPHIIKLYQVISTPTDFFMVMEYVSGGELFDYICKHGRVEEMEARRLFQQILSAVDYCHRHMVVHRDLKPENVLLDAHMNAKIADFGLSNMMSDGEFLRTSCGSPNYAAPEVISGRLYAGPEVDIWSCGVILYALLCGTLPFDDEHVPTLFKKIRGGVFYIPEYLNRSVATLLMHMLQVDPLKRATIKDIREHEWFKQDLPSYLFPEDPSYDANVIDDEAVKEVCEKFECTESEVMNSLYSGDPQDQLAVAYHLIIDNRRIMNQASEFYLASSPPSGSFMDDSAMHIPPGLKPHPERMPPLIADSPKARCPLDALNTTKPKSLAVKKAKWHLGIRSQSKPYDIMAEVYRAMKQLDFEWKVVNAYHLRVRRKNPVTGNYVKMSLQLYLVDNRSYLLDFKSIDDEVVEQRSGSSTPQRSCSAAGLHRPRSSFDSTTAESHSLSGSLTGSLTGSTLSSVSPRLGSHTMDFFEMCASLITTLAR
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.63
R work: 0.1779
R free: 0.2296
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.2
Crystallization temperature (K): 277
Crystal growth procedure: 12% PEG3350, 300 mM Guanidine in 100mM PIPES buffer at pH 7.2.
Matthews coefficient: 2.55
Solvent content (%): 51.79
Ligand: STAUROSPORINE (STU)
Ligand formula: C28 H26 N4 O3
Ligand molecular weight: 466.531
Ligand SMILES: CC12C(C(CC(O1)n3c4ccccc4c5c3c6n2c7ccccc7c6c8c5C(=O)NC8)NC)OC
Ligand InChI: InChI=1S/C28H26N4O3/c1-28-26(34-3)17(29-2)12-20(35-28)31-18-10-6-4-8-14(18)22-23-16(13-30-27(23)33)21-15-9-5-7-11-19(15)32(28)25(21)24(22)31/h4-11,17,20,26,29H,12-13H2,1-3H3,(H,30,33)/t17-,20-,26-,28+/m1/s1
Release date: 2017-03-29
CRYSTAL STRUCTURE OF HUMAN HPK1 (MAP4K1) COMPLEX WITH 2-[8-Amino-7-fluoro-6-(8-methyl-2,3-dihydro-1H-pyrido[2,3-b][1,4]oxazin-7-yl)-isoquinolin-3-ylamino]-6-isopropyl-5,6-dihydro-4H-1,6,8a-triaza-azulen-7-one (PDB entry 8CIJ)
Macromolecule: Mitogen-activated protein kinase kinase kinase kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 307 residues
Sequence: MDVVDPDIFNRDPRDHYDLLQRLGGGTYGEVFKARDKVSGDLVALKMVKMEPDDDVSTLQKEILILKTCRHANIVAYHGSYLWLQKLWICMEFCGAGSLQDIYQVTGSLSELQISYVCREVLQGLAYLHSQKKIHRDIKGANILINDAGEVRLADFGISAQIGAELARRLEFIGTPYWMAPEVAAVALKGGYNELCDIWSLGITAIELAELQPPLFDVHPLRVLFLMTKSGYQPPRLKEKGKWSAAFHNFIKVTLTKSPKKRPSATKMLSHQLVSQPGLNRGLILDLLDKLKNPGKGPSIGDIEDEE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.821
R work: 0.2373
R free: 0.266
Average B factor: 97.68
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 10 % PEG 4000, 120 mM NaCl, 01. M HEPES, pH = 7.75
Matthews coefficient: 2.77
Solvent content (%): 55.62
Ligand: 2-[[8-azanyl-7-fluoranyl-6-(8-methyl-2,3-dihydro-1~{H}-pyrido[2,3-b][1,4]oxazin-7-yl)isoquinolin-3-yl]amino]-6-propan-2-yl-5,8-dihydro-4~{H}-pyrazolo[1,5-d][1,4]diazepin-7-one (USF)
Ligand formula: C27 H29 F N8 O2
Ligand molecular weight: 516.57
Ligand SMILES: Cc1c(cnc2c1NCCO2)c3cc4cc(ncc4c(c3F)N)Nc5cc6n(n5)CC(=O)N(CC6)C(C)C
Ligand InChI: InChI=1S/C27H29FN8O2/c1-14(2)35-6-4-17-10-22(34-36(17)13-23(35)37)33-21-9-16-8-18(24(28)25(29)20(16)12-31-21)19-11-32-27-26(15(19)3)30-5-7-38-27/h8-12,14,30H,4-7,13,29H2,1-3H3,(H,31,33,34)
Release date: 2023-08-16
Crystal structure of JmjC domain of human histone demethylase UTY in complex with epitherapuetic compound 2-(((2-((2-(dimethylamino)ethyl) (ethyl)amino)-2-oxoethyl)amino)methyl)isonicotinic acid. (PDB entry 4UF0)
Macromolecule: HISTONE DEMETHYLASE UTY
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 478 residues
Sequence: MLPKDKLNPPTPSIYLENKRDAFFPPLHQFCTNPKNPVTVIRGLAGALKLDLGLFSTKTLVEANNEHMVEVRTQLLQPADENWDPTGTKKIWRCESNRSHTTIAKYAQYQASSFQESLREENEKRTQHKDHSDNESTSSENSGRRRKGPFKTIKFGTNIDLSDNKKWKLQLHELTKLPAFARVVSAGNLLTHVGHTILGMNTVQLYMKVPGSRTPGHQENNNFCSVNINIGPGDCEWFVVPEDYWGVLNDFCEKNNLNFLMSSWWPNLEDLYEANVPVYRFIQRPGDLVWINAGTVHWVQAVGWCNNIAWNVGPLTACQYKLAVERYEWNKLKSVKSPVPMVHLSWNMARNIKVSDPKLFEMIKYCLLKILKQYQTLREALVAAGKEVIWHGRTNEEPAHYCSICEVEVFNLLFVTNESNTQKTYIVHCHDCARKTSKSLENFVVLEQYKMEDLIQVYDQFTLALSLSSSSAENLYFQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.78
R work: 0.14857
R free: 0.21517
Average B factor: 36.64
Crystallization pH: 6.5
Crystal growth procedure: 25% PEG3350, 0.1M BIS-TRIS PH 6.5
Matthews coefficient: 2.83
Solvent content (%): 56.56
Ligand: FE (II) ION (FE2)
Ligand formula: Fe
Ligand molecular weight: 55.845
Ligand SMILES: [Fe+2]
Ligand InChI: InChI=1S/Fe/q+2
Release date: 2015-01-14
Human cyclophilin A bound to a series of acylcic and macrocyclic inhibitors: (2R,5S,11S,14S,18E)-2,11-dimethyl-14-(propan-2-yl)-3-oxa-9,12,15,21,29-pentaazatetracyclo[18.5.3.1~5,9~.0~23,27~]nonacosa-1(26),18,20,22,24,27-hexaene-4,10,13,16-tetrone (compound 21) (PDB entry 6X4O)
Macromolecule: Peptidyl-prolyl cis-trans isomerase A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 167 residues
Sequence: GHMVNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFGSRNGKTSKKITIADCGQLE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.5
R work: 0.178
R free: 0.1984
Average B factor: 22.39
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 277
Crystal growth procedure: 20 mM Tris-HCl, pH 8.5, 2 mM DTT, 2 mM EDTA, 20-35% PEG3350, 5% ethanol
Matthews coefficient: 2.74
Solvent content (%): 55.19
Ligand: (2R,5S,11S,14S,18E)-2,11-dimethyl-14-(propan-2-yl)-3-oxa-9,12,15,21,29-pentaazatetracyclo[18.5.3.1~5,9~.0~23,27~]nonacosa-1(26),18,20,22,24,27-hexaene-4,10,13,16-tetrone (UO7)
Ligand formula: C28 H35 N5 O5
Ligand molecular weight: 521.608
Ligand SMILES: CC1c2ccc3cnc(cc3c2)C=CCC(=O)NC(C(=O)NC(C(=O)N4CCCC(N4)C(=O)O1)C)C(C)C
Ligand InChI: InChI=1S/C28H35N5O5/c1-16(2)25-26(35)30-17(3)27(36)33-12-6-8-23(32-33)28(37)38-18(4)19-10-11-20-15-29-22(14-21(20)13-19)7-5-9-24(34)31-25/h5,7,10-11,13-18,23,25,32H,6,8-9,12H2,1-4H3,(H,30,35)(H,31,34)/b7-5+/t17-,18+,23-,25-/m0/s1
Release date: 2020-06-24
Titin FnIII-domain I109-I111 (I/A4-A/A6) from the MIR region (PDB entry 8BXR)
Macromolecule: Titin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 300 residues
Sequence: GAMEPTMDLSAFKDGLEVIVPNPITTLVPSTGYPRPTATWCFGDKVLETGDRVKMKTLSAYAELVISPSERSDKGIYTLKLENRVKTISGEIDVNVIARPSAPKELKFGDITKDSVHLTWEPPDDDGGSPLTGYVVEKREVSRKTWTKVMDFVTDLEFTVPDLVQGKEYLFRVCARNKCGPGEPAYVDEPVNMSTPATVPDPPENVKWRDRTANSIFLTWDPPKNDGGSRIKGYIVERCPRGSDKWVACGEPVAETKMEVTGLEEGKWYAYRVKALNRQGASKPSRPTEEIQAVDTQEAP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.7
R work: 0.2254
R free: 0.2714
Average B factor: 69.26
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291.15
Crystal growth procedure: 0.1M MES pH 6, 10% [w/v] PEG 6000
Matthews coefficient: 2.61
Solvent content (%): 52.9
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: 2023-02-15
Crystal structure of human N6amt1-Trm112 in complex with SAM (space group P6122) (PDB entry 6KMR)
Macromolecule: Multifunctional methyltransferase subunit TRM112-like protein
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 126 residues
Sequence: MMKLLTHNLLSSHVRGVGSRGFPLRLQATEVRICPVEFNPNFVARMIPKVEWSAFLEAADNLRLIQVPKGPVEGYEENEEFLRTMHHLLLEVEVIEGTLQCPESGRMFPISRGIPNMLLSEEETES
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.1617
R free: 0.1918
Average B factor: 37.9946
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 289
Crystal growth procedure: 0.1M succinic acid, pH 7.0, 15% PEG 3350
Matthews coefficient: 2.92
Solvent content (%): 61.68
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: 2019-09-18
Crystal structure of the GSK-3/Axin complex bound to a phosphorylated beta-catenin T41A peptide (PDB entry 8VME)
Macromolecule: Glycogen synthase kinase-3 beta
Type: Protein, polypeptide(L)
Source organism: Mus musculus
EC number: 2.7.11.26
Sequence length: 365 residues
Sequence: QMKVSRDKDGSKVTTVVATPGQGPDRPQEVSYTDTKVIGNGSFGVVYQAKLCDSGELVAIKKVLQDKRFKNRELQIMRKLDHCNIVRLRYFFYSSGEKKDEVYLNLVLDYVPETVYRVARHYSRAKQTLPVIYVKLYMYQLFRSLAYIHSFGICHRDIKPQNLLLDPDTAVLKLCDFGSAKQLVRGEPNVSYICSRYYRAPELIFGATDYTSSIDVWSAGCVLAELLLGQPIFPGDSGVDQLVEIIKVLGTPTREQIREMNPNYTEFKFPQIKAHPWTKVFRPRTPPEAIALCSRLLEYTPTARLTPLEACAHSFFDELRDPNVKLPNGRDTPALFNFTTQELSSNPPLATILIPPHARHHHHHH
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R free: 0.2298
Average B factor: 72.36
Crystallization method: MICRODIALYSIS
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 10% PEG35000, 20 mM Tris, pH 7.5, 300 mM sodium chloride, 5% glycerol, 10 mM magnesium chloride, 200 uM ATP, 5 mM DTT
Matthews coefficient: 2.93
Solvent content (%): 58.01
Ligand: ADENOSINE-5'-DIPHOSPHATE (ADP)
Ligand formula: C10 H15 N5 O10 P2
Ligand molecular weight: 427.201
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
Ligand InChI: InChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
Release date: 2024-08-28
Structure of human DPP3 in complex with angiotensin-II (PDB entry 5E2Q)
Macromolecule: Dipeptidyl peptidase 3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.14.4
Sequence length: 726 residues
Sequence: MADTQYILPNDIGVSSLDSREAFRLLSPTERLYAYHLSRAAWYGGLAVLLQTSPEAPYIYALLSRLFRAQDPDQLRQHALAEGLTEEEYQAFLVYAAGVYSNMGNYKSFGDTKFVPNLPKEKLERVILGSEAAQQHPEEVRGLWQTCGELMFSLEPRLRHLGLGKEGITTYFSGNCTMEDAKLAQDFLDSQNLSAYNTRLFKEVDGCGKPYYEVRLASVLGSEPSLDSEVTSKLKSYEFRGSPFQVTRGDYAPILQKVVEQLEKAKAYAANSHQGQMLAQYIESFTQGSIEAHKRGSRFWIQDKGPIVESYIGFIESYRDPFGSRGEFEGFVAVVNKAMSAKFERLVASAEQLLKELPWPPTFEKDKFLTPDFTSLDVLTFAGSGIPAGINIPNYDDLRQTEGFKNVSLGNVLAVAYATQREKLTFLEEDDKDLYILWKGPSFDVQVGLHALLGHGSGKLFVQDEKGAFNFDQETVINPETGEQIQSWYRCGETWDSKFSTIASSYEECRAESVGLYLSLHPQVLEIFGFEGADAEDVIYVNWLNMVRAGLLALEFYTPEAFNWRQAHMQARFVILRVLLEAGEGLVTITPTTGSDGRPDARVRLDRSKIRSVGKPALERFLRRLQVLKSTGDVAGGRALYEGYATVTDAPPESFLTLRDTVLLRKESRKLIVQPNTRLEGSDVQLLEYEASAAGLIRSFSERFPEDGPELEEILTQLATADARFW
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.404
R work: 0.2062
R free: 0.2473
Average B factor: 38.5
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.2
Crystallization temperature (K): 293
Crystal growth procedure: 0.056 M sodium phosphate monobasic monohydrate, 1.344 M potassium phosphate dibasic monohydrate
Matthews coefficient: 2.49
Solvent content (%): 50.58
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: 2016-04-13
Crystal Structure of the Human CAMKK2B bound to a thiadiazinone benzamide inhibitor (PDB entry 5VT1)
Macromolecule: Calcium/calmodulin-dependent protein kinase kinase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.17
Sequence length: 291 residues
Sequence: SMQLNQYTLKDEIGKGSYGVVKLAYNENDNTYYAMKVLSKKKLIRQAGFPRRPPPRGTRPAPGGCIQPRGPIEQVYQEIAILKKLDHPNVVKLVEVLDDPNEDHLYMVFELVNQGPVMEVPTLKPLSEDQARFYFQDLIKGIEYLHYQKIIHRDIKPSNLLVGEDGHIKIADFGVSNEFKGSDALLSNTVGTPAFMAPESLSETRKIFSGKALDVWAMGVTLYCFVFGQCPFMDERIMCLHSKIKSQALEFPDQPDIAEDLKDLITRMLDKNPESRIVVPEIKLHPWVTRH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.161
R free: 0.185
Average B factor: 33.95
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 24% PEG 8000, 0.1M magnesium acetate, 0.1M CHC buffer (citric acid, ches, hepes).
Matthews coefficient: 3.06
Solvent content (%): 59.85
Ligand: 4-({5-[(3-hydroxy-4-methylphenyl)amino]-4-oxo-4H-1,2,6-thiadiazin-3-yl}amino)benzamide (9JS)
Ligand formula: C17 H15 N5 O3 S
Ligand molecular weight: 369.398
Ligand SMILES: Cc1ccc(cc1O)NC2=NSN=C(C2=O)Nc3ccc(cc3)C(=O)N
Ligand InChI: InChI=1S/C17H15N5O3S/c1-9-2-5-12(8-13(9)23)20-17-14(24)16(21-26-22-17)19-11-6-3-10(4-7-11)15(18)25/h2-8,23H,1H3,(H2,18,25)(H,19,21)(H,20,22)
Release date: 2017-05-24
Carbonic Anhydrase II in complex with Sulfonamide Inhibitor (PDB entry 5EIJ)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 257 residues
Sequence: HWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.99
R work: 0.1586
R free: 0.2188
Average B factor: 15.8026
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 298
Crystal growth procedure: 1.6M sodium citrate, 50mM Tris
Matthews coefficient: 2.15
Solvent content (%): 42.86
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: 2016-11-09
Polymerase Eta-catalyzed insertion of correct G opposite template cytarabine (AraC) residue (PDB entry 6PZ3)
Macromolecule: DNA polymerase eta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 435 residues
Sequence: GPHMATGQDRVVALVDMDCFFVQVEQRQNPHLRNKPCAVVQYKSWKGGGIIAVSYEARAFGVTRSMWADDAKKLCPDLLLAQVRESRGKANLTKYREASVEVMEIMSRFAVIERASIDEAYVDLTSAVQERLQKLQGQPISADLLPSTYIEGLPQGPTTAEETVQKEGMRKQGLFQWLDSLQIDNLTSPDLQLTVGAVIVEEMRAAIERETGFQCSAGISHNKVLAKLACGLNKPNRQTLVSHGSVPQLFSQMPIRKIRSLGGKLGASVIEILGIEYMGELTQFTESQLQSHFGEKNGSWLYAMCRGIEHDPVKPRQLPKTIGCSKNFPGKTALATREQVQWWLLQLAQELEERLTKDRNDNDRVATQLVVSIRVQGDKRLSSLRRCCALTRYDAHKMSHDAFTVIKNMNTSGIQTEWSPPLTMLFLCATKFSAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.395
R work: 0.1739
R free: 0.2157
Average B factor: 40.9214
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 293
Crystal growth procedure: MES BUFFER, PEG1500
Matthews coefficient: 2.07
Solvent content (%): 40.59
Ligand: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine (XG4)
Ligand formula: C10 H17 N6 O12 P3
Ligand molecular weight: 506.196
Ligand SMILES: c1nc2c(n1C3CC(C(O3)COP(=O)(NP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
Ligand InChI: InChI=1S/C10H17N6O12P3/c11-10-13-8-7(9(18)14-10)12-3-16(8)6-1-4(17)5(27-6)2-26-29(19,20)15-30(21,22)28-31(23,24)25/h3-6,17H,1-2H2,(H2,23,24,25)(H3,11,13,14,18)(H3,15,19,20,21,22)/t4-,5+,6+/m0/s1
Release date: 2019-11-20
CDK2-CyclinE1 in complex with allosteric inhibitor I-198. (PDB entry 8VQ3)
Macromolecule: Cyclin-dependent kinase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.22
Sequence length: 298 residues
Sequence: MENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVPSTAIREISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQDLKKFMDASALTGIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTYTHEVVTLWYRAPEILLGCKYYSTAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGTPDEVVWPGVTSMPDYKPSFPKWARQDFSKVVPPLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPVPHLRL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.84
R work: 0.1993
R free: 0.2169
Average B factor: 46.2
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 295
Crystal growth procedure: 0.21 M sodium citrate tribasic dihydrate, 19.09% PEG3350
Matthews coefficient: 2.9
Solvent content (%): 57.63
Ligand: (8R)-N-[(2S,3R)-3-(cyclohexylmethoxy)-1-(morpholin-4-yl)-1-oxobutan-2-yl]-2-[(1S)-2,2-dimethylcyclopropane-1-carbonyl]-6-(1,3-thiazole-5-carbonyl)-2,6-diazaspiro[3.4]octane-8-carboxamide (A1AC4)
Ligand formula: C32 H47 N5 O6 S
Ligand molecular weight: 629.81
Ligand SMILES: CC(C(C(=O)N1CCOCC1)NC(=O)C2CN(CC23CN(C3)C(=O)C4CC4(C)C)C(=O)c5cncs5)OCC6CCCCC6
Ligand InChI: InChI=1S/C32H47N5O6S/c1-21(43-16-22-7-5-4-6-8-22)26(30(41)35-9-11-42-12-10-35)34-27(38)24-15-36(29(40)25-14-33-20-44-25)17-32(24)18-37(19-32)28(39)23-13-31(23,2)3/h14,20-24,26H,4-13,15-19H2,1-3H3,(H,34,38)/t21-,23-,24?,26+/m1/s1
Release date: 2024-01-31
Crystal structure of an anaplastic lymphoma kinase-derived neuroblastoma tumor antigen bound to the Human Major Histocompatibility Complex Class I molecule HLA-B*1501 (PDB entry 5VZ5)
Macromolecule: Tyrosine-protein kinase receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 10 residues
Sequence: AQDIYRASYY
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5901
R work: 0.2158
R free: 0.2653
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 295
Crystal growth procedure: 0.1M Hepes (7.5)
2M Ammonium sulfate
2% PEG400
Matthews coefficient: 3.63
Solvent content (%): 66
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: 2018-03-21
DNA polymerase beta ternary product complex with 8-oxoG:C and inserted dCTP (PDB entry 5V1I)
Macromolecule: DNA (5'-D(*CP*CP*GP*AP*CP*GP*CP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
Type: DNA, polydeoxyribonucleotide
Source organism: synthetic construct
Sequence length: 16 residues
Sequence: CCGACGCCGCATCAGC
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.035
R work: 0.184
R free: 0.2374
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8
Crystallization temperature (K): 291
Crystal growth procedure: 50 mM imidazole, 350 mM sodium chloride, 17% PEG3350
Matthews coefficient: 2.27
Solvent content (%): 45.92
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: 2017-05-10
TRIM7 in complex with C-terminal peptide of 2C (PDB entry 7W0Q)
Macromolecule: E3 ubiquitin-protein ligase TRIM7
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.27
Sequence length: 174 residues
Sequence: KEEKVELTLDPDTANPRLILSLDLKGVRLGERAQDLPNHPCRFDTNTRVLASCGFSSGRHHWEVEVGSKDGWAFGVARESVRRKGLTPFTPEEGVWALQLNGGQYWAVTSPERSPLSCGHLSRVRVALDLEVGAVSFYAVEDMRHLYTFRVNFQERVFPLFSVCSTGTYLRIWP
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.1
R work: 0.1857
R free: 0.2112
Average B factor: 15.02
Crystallization method: LIQUID DIFFUSION
Crystallization temperature (K): 291.15
Crystal growth procedure: PEG 3350, potassium nitrate
Matthews coefficient: 2.11
Solvent content (%): 41.67
Release date: 2022-08-10
Structure of Optineurin bound to HOIP NZF1 domain and M1-linked diubiquitin, crystal form 1 (PDB entry 9B12)
Macromolecule: Optineurin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 96 residues
Sequence: GPDRAVLKELSEKLELAEKALASKQLQMDEMKQTIAKQEEDLETMTILRAQMEVYCSDFHAERAAREKIHEEKEQLALQLAVLLKENDAFEDGGRQ
Oligomeric state: Hetero 5-mer
Stoichiometry: A2, B2, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.81
R work: 0.2313
R free: 0.2685
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 3:1 with reservoir solution containing 50% PEG 200 and 0.1 M HEPES pH 7.5
Ligand: TETRAETHYLENE GLYCOL (PG4)
Ligand formula: C8 H18 O5
Ligand molecular weight: 194.226
Ligand SMILES: C(COCCOCCOCCO)O
Ligand InChI: InChI=1S/C8H18O5/c9-1-3-11-5-7-13-8-6-12-4-2-10/h9-10H,1-8H2
Release date: 2024-07-31
MAGE-A3 Reactive TCR in complex with Titin Epitope in HLA-A1 (PDB entry 5BS0)
Macromolecule: Beta-2-microglobulin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 100 residues
Sequence: MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM
Oligomeric state: Hetero 5-mer
Stoichiometry: A1, B1, C1, D1, E1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.4
R work: 0.203
R free: 0.2621
Average B factor: 56.084
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 291
Crystal growth procedure: 0.2M Ammonium Chloride, 0.1M MES, 20% PEG 4000
Matthews coefficient: 2.5
Solvent content (%): 50.72
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: 2016-03-02