satarupa22/MacromolecularLigandDB huggingface dataset:
Structure of SARS-CoV-2 Gamma variant spike receptor-binding domain complexed with human ACE2 (PDB entry 7EKC)
Macromolecule: Angiotensin-converting enzyme 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.17.23
Sequence length: 603 residues
Sequence: STIEEQAKTFLDKFNHEAEDLFYQSSLASWNYNTNITEENVQNMNNAGDKWSAFLKEQSTLAQMYPLQEIQNLTVKLQLQALQQNGSSVLSEDKSKRLNTILNTMSTIYSTGKVCNPDNPQECLLLEPGLNEIMANSLDYNERLWAWESWRSEVGKQLRPLYEEYVVLKNEMARANHYEDYGDYWRGDYEVNGVDGYDYSRGQLIEDVEHTFEEIKPLYEHLHAYVRAKLMNAYPSYISPIGCLPAHLLGDMWGRFWTNLYSLTVPFGQKPNIDVTDAMVDQAWDAQRIFKEAEKFFVSVGLPNMTQGFWENSMLTDPGNVQKAVCHPTAWDLGKGDFRILMCTKVTMDDFLTAHHEMGHIQYDMAYAAQPFLLRNGANEGFHEAVGEIMSLSAATPKHLKSIGLLSPDFQEDNETEINFLLKQALTIVGTLPFTYMLEKWRWMVFKGEIPKDQWMKKWWEMKREIVGVVEPVPHDETYCDPASLFHVSNDYSFIRYYTRTLYQFQFQEALCQAAKHEGPLHKCDISNSTEAGQKLFNMLRLGKSEPWTLALENVVGAKNMNVRPLLNYFEPLFTWLKDQNKNSFVGWSTDWSPYADHHHHHH
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.8
R work: 0.2141
R free: 0.2252
Average B factor: 53.64
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 291
Crystal growth procedure: 0.1 M MES, pH 6.5, 12% w/v PEG 20000
Matthews coefficient: 3.2
Solvent content (%): 61.53
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: 2021-11-03
The crystal structure of human abl1 kinase domain in complex with abl1-A-EBA (PDB entry 8H7H)
Macromolecule: Tyrosine-protein kinase ABL1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 277 residues
Sequence: GAMGSSPNYDKWEMERTDITMKHKLGGGQYGEVYEGVWKKYSLTVAVKTLKEDTMEVEEFLKEAAVMKEIKHPNLVQLLGVCTREPPFYIITEFMTYGNLLDYLRECNRQEVNAVVLLYMATQISSAMEYLEKKNFIHRDLAARNCLVGENHLVKVADFGLSRLMTGDTYTAHAGAKFPIKWTAPESLAYNKFSIKSDVWAFGVLLWEIATYGMSPYPGIDLSQVYELLEKDYRMERPEGCPEKVYELMRACWQWNPSDRPSFAEIHQAFETMFQES
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.27789711576
R work: 0.182442800513
R free: 0.220547655789
Average B factor: 25.6573189228
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 1.5 M (NH4)2SO4, 0.1 M HEPES (pH 7.0) and 4% v/v 1,3-propanediol
Matthews coefficient: 3.06
Solvent content (%): 59.85
Ligand: 5-[3-(6-methoxyisoquinolin-7-yl)-1H-pyrrolo[2,3-b]pyridin-5-yl]-N-methyl-N-prop-2-ynyl-pyridine-3-carboxamide (QH9)
Ligand formula: C27 H21 N5 O2
Ligand molecular weight: 447.488
Ligand SMILES: CN(CC#C)C(=O)c1cc(cnc1)c2cc3c(c[nH]c3nc2)c4cc5cnccc5cc4OC
Ligand InChI: InChI=1S/C27H21N5O2/c1-4-7-32(2)27(33)21-8-18(13-29-14-21)20-10-23-24(16-31-26(23)30-15-20)22-9-19-12-28-6-5-17(19)11-25(22)34-3/h1,5-6,8-16H,7H2,2-3H3,(H,30,31)
Release date: 2023-03-22
Crystal structure of human ATAD2 bromodomain in complex with 8-2-(dimethylamino)ethylamino-3-methyl-1,2-dihydroquinolin-2-one (PDB entry 5A5P)
Macromolecule: ATPASE FAMILY AAA DOMAIN-CONTAINING PROTEIN 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.3
Sequence length: 130 residues
Sequence: SMQEEDTFRELRIFLRNVTHRLAIDKRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNPDRDPGDRLIRHRACALRDTAYAIIKEELDEDFEQLCEEIQESR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.03
R work: 0.18759
R free: 0.20805
Average B factor: 28.414
Crystal growth procedure: 0.1M TRISHCL PH 7.0-8.0, 1.2-1.5M AMMONIUM SULPHATE,20-25% PEG3350
Matthews coefficient: 4.03
Solvent content (%): 69.48
Ligand: 8-{[2-(dimethylamino)ethyl]amino}-3-methyl-1,2-dihydroquinolin-2-one (JTF)
Ligand formula: C14 H19 N3 O
Ligand molecular weight: 245.32
Ligand SMILES: CC1=Cc2cccc(c2NC1=O)NCCN(C)C
Ligand InChI: InChI=1S/C14H19N3O/c1-10-9-11-5-4-6-12(13(11)16-14(10)18)15-7-8-17(2)3/h4-6,9,15H,7-8H2,1-3H3,(H,16,18)
Release date: 2015-07-22
Multiconformer synchrotron model of CypA at 180 K (PDB entry 4YUI)
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): 1.38
R work: 0.133
R free: 0.1747
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: 2.71
Solvent content (%): 54.69
Release date: 2015-10-14
First SH3 domain of POSH (Plenty of SH3 Domains protein) (PDB entry 7NZC)
Macromolecule: E3 ubiquitin-protein ligase SH3RF1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.27
Sequence length: 63 residues
Sequence: GRRQLPCAKALYNYEGKEPGDLKFSKGDIIILRRQVDENWYHGEVNGIHGFFPTNFVQIIKPL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.111
R work: 0.1468
R free: 0.1775
Average B factor: 17.845
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 8
Crystallization temperature (K): 293
Crystal growth procedure: 0.2 M NaF, 22% PEG 3350
Matthews coefficient: 2.4
Solvent content (%): 47.5
Ligand: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID (EPE)
Ligand formula: C8 H18 N2 O4 S
Ligand molecular weight: 238.305
Ligand SMILES: C1CN(CCN1CCO)CCS(=O)(=O)O
Ligand InChI: InChI=1S/C8H18N2O4S/c11-7-5-9-1-3-10(4-2-9)6-8-15(12,13)14/h11H,1-8H2,(H,12,13,14)
Release date: 2021-12-22
Crystal structure of potent human Dihydroorotate Dehydrogenase inhibitors based on hydroxylated azole scaffolds (PDB entry 5MVD)
Macromolecule: Dihydroorotate dehydrogenase (quinone), mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.3.5.2
Sequence length: 363 residues
Sequence: DERFYAEHLMPTLQGLLDPESAHRLAVRFTSLGLLPRARFQDSDMLEVRVLGHKFRNPVGIAAGFDKHGEAVDGLYKMGFGFVEIGSVTPKPQEGNPRPRVFRLPEDQAVINRYGFNSHGLSVVEHRLRARQQKQAKLTEDGLPLGVNLGKNKTSVDAAEDYAEGVRVLGPLADYLVVNVSSPNTAGLRSLQGKAELRRLLTKVLQERDGLRRVHRPAVLVKIAPDLTSQDKEDIASVVKELGIDGLIVTNTTVSRPAGLQGALRSETGGLSGKPLRDLSTQTIREMYALTQGRVPIIGVGGVSSGQDALEKIRAGASLVQLYTALTFWGPPVVGKVKRELEALLKEQGFGGVTDAIGADHRR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.95
R work: 0.1672
R free: 0.2016
Average B factor: 16.4273
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5
Crystallization temperature (K): 293
Crystal growth procedure: 0.2M KBr, 0.2M KSCN, 0.1M NaAc pH 5.2, 35% PEG 400, 5% PGA-LM
Matthews coefficient: 3.87
Solvent content (%): 68.22
Ligand: OROTIC ACID (ORO)
Ligand formula: C5 H4 N2 O4
Ligand molecular weight: 156.096
Ligand SMILES: C1=C(NC(=O)NC1=O)C(=O)O
Ligand InChI: InChI=1S/C5H4N2O4/c8-3-1-2(4(9)10)6-5(11)7-3/h1H,(H,9,10)(H2,6,7,8,11)
Release date: 2017-03-08
Crystal structure of the G domain of human guanylate-binding protein 2 (hGBP2) in complex with GDP (PDB entry 6VKJ)
Macromolecule: Guanylate-binding protein 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5
Sequence length: 305 residues
Sequence: INLPGPMSLIDNTKGQLVVNPEALKILSAITQPVVVVAIVGLYRTGKSYLMNKLAGKKNGFSLGSTVKSHTKGIWMWCVPHPKKPEHTLVLLDTEGLGDIEKGDNENDSWIFALAILLSSTFVYNSMGTINQQAMDQLHYVTELTDRIKANSSPGNNSVDDSADFVSFFPAFVWTLRDFTLELEVDGEPITADDYLELSLKLRKGTDKKSKSFNDPRLCIRKFFPKRKCFVFDWPAPKKYLAHLEQLKEEELNPDFIEQVAEFCSYILSHSNVKTLSGGIPVNGPRLESLVLTYVNAISSGDLPC
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.105
R work: 0.1809
R free: 0.226
Average B factor: 54.1373
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 289.15
Crystal growth procedure: 0.04M KH2PO4, 12% PEG 8000, 18% glycerol
Matthews coefficient: 2.99
Solvent content (%): 58.9
Ligand: GUANOSINE-5'-DIPHOSPHATE (GDP)
Ligand formula: C10 H15 N5 O11 P2
Ligand molecular weight: 443.201
Ligand SMILES: c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
Ligand InChI: InChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
Release date: 2021-01-27
Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with DXDKDED motif of Myelin transcription factor 1 (PDB entry 7Q45)
Macromolecule: E3 ubiquitin-protein ligase HERC2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.26
Sequence length: 405 residues
Sequence: GAMGSLIRKKAAGLESAATIRTKVFVWGLNDKDQLGGLKGSKIKVPSFSETLSALNVVQVAGGSKSLFAVTVEGKVYACGEATNGRLGLGISSGTVPIPRQITALSSYVVKKVAVHSGGRHATALTVDGKVFSWGEGDDGKLGHFSRMNCDKPRLIEALKTKRIRDIACGSSHSAALTSSGELYTWGLGEYGRLGHGDNTTQLKPKMVKVLLGHRVIQVACGSRDAQTLALTDEGLVFSWGDGDFGKLGRGGSEGCNIPQNIERLNGQGVCQIECGAQFSLALTKSGVVWTWGKGDYFRLGHGSDVHVRKPQVVEGLRGKKIVHVAVGALHCLAVTDSGQVYAWGDNDHGQQGNGTTTVNRKPTLVQGLEGQKITRVACGSSHSVAWTTVDVATPSVHEPVLFQT
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.09999588083
R work: 0.184268613443
R free: 0.22436902922
Average B factor: 35.8498423392
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 8
Crystallization temperature (K): 293.15
Crystal growth procedure: hanging drop
20% PEG 3350
0.18M tris amonium citrate
Matthews coefficient: 2.96
Solvent content (%): 58.43
Ligand: CITRIC ACID (CIT)
Ligand formula: C6 H8 O7
Ligand molecular weight: 192.124
Ligand SMILES: C(C(=O)O)C(CC(=O)O)(C(=O)O)O
Ligand InChI: InChI=1S/C6H8O7/c7-3(8)1-6(13,5(11)12)2-4(9)10/h13H,1-2H2,(H,7,8)(H,9,10)(H,11,12)
Release date: 2022-11-16
Crystal Structure Of Aldose Reductase (AKR1B1) Complexed With NADP+ And AT-003 (PDB entry 8FH7)
Macromolecule: Aldo-keto reductase family 1 member B1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.1.1.300
Sequence length: 316 residues
Sequence: MASRLLLNNGAKMPILGLGTWKSPPGQVTEAVKVAIDVGYRHIDCAHVYQNENEVGVAIQEKLREQVVKREELFIVSKLWCTYHEKGLVKGACQKTLSDLKLDYLDLYLIHWPTGFKPGKEFFPLDESGNVVPSDTNILDTWAAMEELVDEGLVKAIGISNFNHLQVEMILNKPGLKYKPAVNQIECHPYLTQEKLIQYCQSKGIVVTAYSPLGSPDRPWAKPEDPSLLEDPRIKAIAAKHNKTTAQVLIRFPMQRNLVVIPKSVTPERIAENFKVFDFELSSQDMTTLLSYNRNWRVCALLSCTSHKDYPFHEEF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.45
R work: 0.1451
R free: 0.1689
Average B factor: 16.608
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 298
Crystal growth procedure: 25%PEG 3,350, 100 mM Bis-Tris
Matthews coefficient: 2.21
Solvent content (%): 44.22
Ligand: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE (NAP)
Ligand formula: C21 H28 N7 O17 P3
Ligand molecular weight: 743.405
Ligand SMILES: c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)OP(=O)(O)O)O)O)O)C(=O)N
Ligand InChI: InChI=1S/C21H28N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1-4,7-8,10-11,13-16,20-21,29-31H,5-6H2,(H7-,22,23,24,25,32,33,34,35,36,37,38,39)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
Release date: 2023-12-20
KALLIKREIN-7 IN COMPLEX WITH COMPOUND1 (PDB entry 5FAH)
Macromolecule: Kallikrein-7
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.117
Sequence length: 224 residues
Sequence: IIDGAPCARGSHPWQVALLSGNQLHCGGVLVNERWVLTAAHCKMNEYTVHLGSDTLGDRRAQRIKASKSFRHPGYSTQTHVNDLMLVKLNSQARLSSMVKKVRLPSRCEPPGTTCTVSGWGTTTSPDVTFPSDLMCVDVKLISPQDCTKVRKDLLENSMLCAGIPDSKKNACNGDSGGPLVCRGTLQGLVSWGTFPCGQPNDPGVYTQVCKFTKWINDTMKKHR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.1
R work: 0.1875
R free: 0.1965
Average B factor: 17.17
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.5 microlitre Protein solution were mixed with 0.5 microlitre RESERVOIR solution. PROTEIN SOLUTION: 24.6 MG/ML KALLIKREIN 7, 50 MM SODIUM ACETATE PH 5.6, 100 MM NACL, 2 MM INHIBITOR, 1.8% DMSO, RESERVOIR SOLUTION: 35% PEG 3350, 100 MM SODIUM ACETATE PH 4.8, 200 MM CALCIUM CHLORIDE. CRYO: FLASH FREEZING IN LIQUID NITROGEN WITHOUT ADDITIONAL CRYO SOLUTION.
Matthews coefficient: 2.12
Solvent content (%): 41.92
Ligand: ACETATE ION (ACT)
Ligand formula: C2 H3 O2
Ligand molecular weight: 59.044
Ligand SMILES: CC(=O)[O-]
Ligand InChI: InChI=1S/C2H4O2/c1-2(3)4/h1H3,(H,3,4)/p-1
Release date: 2016-10-26
crystal structure of the human TGT catalytic subunit QTRT1 in complex with queuine (PDB entry 6H45)
Macromolecule: Queuine tRNA-ribosyltransferase catalytic subunit 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.2.64
Sequence length: 392 residues
Sequence: SAPRIMRLVAECSRSRARAGELWLPHGTVATPVFMPVGTQATMKGITTEQLDALGCRICLGNTYHLGLRPGPELIQKANGLHGFMNWPHNLLTDSGGFQMVSLVSLSEVTEEGVRFRSPYDGNETLLSPEKSVQIQNALGSDIIMQLDDVVSSTVTGPRVEEAMYRSIRWLDRCIAAHQRPDKQNLFAIIQGGLDADLRATCLEEMTKRDVPGFAIGGLSGGESKSQFWRMVALSTSRLPKDKPRYLMGVGYATDLVVCVALGCDMFDCVFPTRTARFGSALVPTGNLQLRKKVFEKDFGPIDPECTCPTCQKHSRAFLHALLHSDNTAALHHLTVHNIAYQLQLMSAVRTSIVEKRFPDFVRDFMGAMYGDPTLCPTWATDALASVGITLG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.4
R work: 0.2013
R free: 0.2396
Average B factor: 58.0269
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 100 mM Tris pH 7.8
200 mM KBr
200 mM KSCN
3 % (w/v) PGA-LM
5 % (w/v) PEG 4000
Matthews coefficient: 2.66
Solvent content (%): 53.7
Ligand: 2-amino-5-({[(1S,4S,5R)-4,5-dihydroxycyclopent-2-en-1-yl]amino}methyl)-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one (QEI)
Ligand formula: C12 H15 N5 O3
Ligand molecular weight: 277.279
Ligand SMILES: c1c(c2c([nH]1)N=C(NC2=O)N)CNC3C=CC(C3O)O
Ligand InChI: InChI=1S/C12H15N5O3/c13-12-16-10-8(11(20)17-12)5(4-15-10)3-14-6-1-2-7(18)9(6)19/h1-2,4,6-7,9,14,18-19H,3H2,(H4,13,15,16,17,20)/t6-,7-,9+/m0/s1
Release date: 2018-09-05
Specific covalent inhibitor of ERK2 (PDB entry 8AOJ)
Macromolecule: Mitogen-activated protein kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.24
Sequence length: 368 residues
Sequence: MAHHHHHHMAAAAAAGAGPEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFEHQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKLLKTQHLSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLLNTTCDLKICDFGLARVADPDHDHTGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILGILGSPSQEDLNCIINLKARNYLLSLPHKNKVPWNRLFPNADSKALDLLDKMLTFNPHKRIEVEQALAHPYLEQYYDPSDEPIAEAPFKFDMELDDLPKEKLKELIFEETARFQPGYRS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.12
R work: 0.1791
R free: 0.2027
Average B factor: 22.533
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.2
Crystallization temperature (K): 293
Crystal growth procedure: 0.2M (NH4)2SO4
33% MPEG 2000
0.02M Mercaptoethanol
0.1M pH=7.2 HEPES/NaOH
Matthews coefficient: 2.31
Solvent content (%): 46.65
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: 2022-09-28
Crystal structure of KDM5B in complex with S49195a. (PDB entry 6EK6)
Macromolecule: Lysine-specific demethylase 5B,Lysine-specific demethylase 5B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 455 residues
Sequence: MFLPPPECPVFEPSWEEFADPFAFIHKIRPIAEQTGICKVRPPPDWQPPFACDVDKLHFTPRIQRLNELEAQTRVRDYTLRTFGEMADAFKSDYFNMPVHMVPTELVEKEFWRLVSTIEEDVTVEYGADIASKEFGSGFPVRDGKIKLSPEEEEYLDSGWNLNNMPVMEQSVLAHITADICGMKLPWLYVGMCFSSFCWHIEDHWSYSINYLHWGEPKTWYGVPGYAAEQLENVMKKLAPELFVSQPDLLHQLVTIMNPNTLMTHEVPVYRTNQCAGEFVITFPRAYHSGFNQGFNFAEAVNFCTVDWLPLGRQCVEHYRLLHRYCVFSHDEMICKMASKADVLDVVVASTVQKDMAIMIEDEKALRETVRKLGVIDSERMDFELLPDDERQCVKCKTTCFMSAISCSCKPGLLVCLHHVKELCSCPPYKYKLRYRYTLDDLYPMMNALKLRAES
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.05
R work: 0.1794
R free: 0.2004
Average B factor: 45.0013
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M HEPES pH 7.5, 0.8M Pottassium Phosphate-dibasic, 0.8M Sodium Phosphate monobasic
Matthews coefficient: 4.17
Solvent content (%): 70.48
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: 2018-03-14
Crystal structure of the human WNK2 CCT-like 1 domain in complex with a WNK1 RFXV peptide (PDB entry 6FBK)
Macromolecule: Serine/threonine-protein kinase WNK2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 98 residues
Sequence: SMAEDTGVRVELAEEDHGRKSTIALRLWVEDPKKLKGKPKDNGAIEFTFDLEKETPDEVAQEMIESGFFHESDVKIVAKSIRDRVALIQWRRERIWPA
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.743
R work: 0.2844
R free: 0.3341
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 20% PEG3350 -- 10% ethylene glycol -- 0.2M sodium fluoride
Matthews coefficient: 2.18
Solvent content (%): 43.45
Release date: 2018-01-24
PanDDA analysis group deposition -- Crystal Structure of JMJD1B in complex with FM001084a (PDB entry 5RAO)
Macromolecule: Lysine-specific demethylase 3B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 372 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSMTSHSWLCDGRLLCLHDPSNKNNWKIFRECWKQGQPVLVSGVHKKLKSELWKPEAFSQEFGDQDVDLVNCRNCAIISDVKVRDFWDGFEIICKRLRSEDGQPMVLKLKDWPPGEDFRDMMPTRFEDLMENLPLPEYTKRDGRLNLASRLPSYFVRPDLGPKMYNAYGLITAEDRRVGTTNLHLDVSDAVNVMVYVGIPIGEGAHDEEVLKTIDEGDADEVTKERIHDHKEKPGALWHIYAAKDAEKIRELLRKVGEEQGQENPPDHDPIHDQSWYLDQTLRKRLYEEYGVQGWAIVQFLGDAVFIPAGAPHQVHNLYSCIKVAEDFVSPEHVKHCFRLTQEFRHLSNTHT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.59
R work: 0.1818
R free: 0.2086
Average B factor: 32.548
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M bis-tris pH 5.5 21% PEG3350  0.3M magnesium chloride
Matthews coefficient: 2.78
Solvent content (%): 55.72
Ligand: ethyl 2-pyridin-4-ylethanoate (S3S)
Ligand formula: C9 H11 N O2
Ligand molecular weight: 165.189
Ligand SMILES: CCOC(=O)Cc1ccncc1
Ligand InChI: InChI=1S/C9H11NO2/c1-2-12-9(11)7-8-3-5-10-6-4-8/h3-6H,2,7H2,1H3
Release date: 2020-04-22
Crystal Structure of HDM2 in complex with Caylin-1 (PDB entry 7QDQ)
Macromolecule: E3 ubiquitin-protein ligase Mdm2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.3.2
Sequence length: 92 residues
Sequence: PASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGDLFGVPSFSVKEHRKIYTMIYRNLVVVN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.26
R work: 0.1821
R free: 0.2162
Average B factor: 18.3177
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6
Crystallization temperature (K): 293
Crystal growth procedure: 2.8M Ammonium Sulfate, 100mM MES
Matthews coefficient: 2.25
Solvent content (%): 45.39
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: 2022-10-05
CRYSTAL STRUCTURE OF HUMAN DNA POLYMERASE ETA INSERTING dAMPNPP ACROSS A DNA TEMPLATE CONTAINING 1,N2-ETHENODEOXYGUANOSINE LESION (PDB entry 5F9L)
Macromolecule: DNA polymerase eta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 435 residues
Sequence: GPHMATGQDRVVALVDMDCFFVQVEQRQNPHLRNKPCAVVQYKSWKGGGIIAVSYEARAFGVTRSMWADDAKKLCPDLLLAQVRESRGKANLTKYREASVEVMEIMSRFAVIERASIDEAYVDLTSAVQERLQKLQGQPISADLLPSTYIEGLPQGPTTAEETVQKEGMRKQGLFQWLDSLQIDNLTSPDLQLTVGAVIVEEMRAAIERETGFQCSAGISHNKVLAKLACGLNKPNRQTLVSHGSVPQLFSQMPIRKIRSLGGKLGASVIEILGIEYMGELTQFTESQLQSHFGEKNGSWLYAMCRGIEHDPVKPRQLPKTIGCSKNFPGKTALATREQVQWWLLQLAQELEERLTKDRNDNDRVATQLVVSIRVQGDKRLSSLRRCCALTRYDAHKMSHDAFTVIKNCNTSGIQTEWSPPLTMLFLCATKFSAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.592
R work: 0.191
R free: 0.2483
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 291
Crystal growth procedure: 0.1 M MES pH 5.5, 5mM magnesium chloride, 22% PEG 2000 MME
Matthews coefficient: 2.12
Solvent content (%): 42
Ligand: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine (DZ4)
Ligand formula: C10 H17 N6 O11 P3
Ligand molecular weight: 490.197
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3CC(C(O3)COP(=O)(NP(=O)(O)OP(=O)(O)O)O)O)N
Ligand InChI: InChI=1S/C10H17N6O11P3/c11-9-8-10(13-3-12-9)16(4-14-8)7-1-5(17)6(26-7)2-25-28(18,19)15-29(20,21)27-30(22,23)24/h3-7,17H,1-2H2,(H2,11,12,13)(H2,22,23,24)(H3,15,18,19,20,21)/t5-,6+,7+/m0/s1
Release date: 2016-12-21
HDAC2 in complex with an inhibitor (PDB entry 7ZZO)
Macromolecule: Histone deacetylase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.1.98
Sequence length: 498 residues
Sequence: MAYSQGGGKKKVCYYYDGDIGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKATAEEMTKYHSDEYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVAGAVKLNRQQTDMAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNFPMRDGIDDESYGQIFKPIISKVMEMYQPSAVVLQCGADSLSGDRLGCFNLTVKGHAKCVEVVKTFNLPLLMLGGGGYTIRNVARCWTYETAVALDCEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTPEYMEKIKQRLFENLRMLPHAPGVQMQAIPEDAVHEDSGDEDGEDPDKRISIRASDKRIACDEEFSDSEDEGEGGRRNVADHKKGAKKARIEEDKKETEDKKTDVKEEDKSKDNSGEKTDTKGTKSEQLSNPGSSGHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.0
R work: 0.1718
R free: 0.225
Average B factor: 25.66
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 38% PEG 300
0.1M pH=8.8 CHES/NaOH
Matthews coefficient: 2.47
Solvent content (%): 50.14
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: 2022-09-21
Structure of a lysozyme antibody complex (PDB entry 4TSB)
Macromolecule: Lysozyme C
Type: Protein, polypeptide(L)
Source organism: Gallus gallus
EC number: 3.2.1.17
Sequence length: 129 residues
Sequence: KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQAWIRGCRL
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.95
R work: 0.1937
R free: 0.2267
Average B factor: 23.59
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 100mM PCPT pH 5.5, 200mM MgCl2, 22 % w/v PEG 3350
Matthews coefficient: 2.34
Solvent content (%): 47.44
Release date: 2015-07-08