satarupa22/MacromolecularLigandDB huggingface dataset:
Wild type APOBEC3A in complex with TT(FdZ)-hairpin inhibitor (crystal form 2) (PDB entry 8FIJ)
Macromolecule: DNA dC->dU-editing enzyme APOBEC-3A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.4.38
Sequence length: 199 residues
Sequence: MEASPASGPRHLMDPHIFTSNFNNGIGRHKTYLCYEVERLDNGTSVKMDQHRGFLHNQAKNLLCGFYGRHAELRFLDLVPSLQLDPAQIYRVTWFISWSPCFSWGCAGEVRAFLQENTHVRLRIFAARIYDYDPLYKEALQMLRDAGAQVSIMTYDEFKHCWDTFVDHQGCPFQPWDGLDEHSQALSGRLRAILQNQGN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.799
R work: 0.2577
R free: 0.3182
Average B factor: 60.975
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 285
Crystal growth procedure: A3A-E72A (50 mM MES pH 6.0, 100 mM NaCl, 1 mM TCEP, 0.2 mM EDTA) was mixed with oligonucleotides (10 mM Tris/HCl pH 7.9, 1 mM EDTA) at 0.85 mM and 1.7 mM respectively. Dilution was done with protein buffer. The mixture was added to crystallization liquid 1 to 1 and the mixture was pipetted on siliconized glass disks and sealed on top of a reservoir of crystallization liquid for hanging drop crystallization at 12 degrees Celsius. The crystallization liquid has the following composition: 100 mM Bicine at  pH 6.6, 200 mM NaCl, 20 mM putrescine, 1 mM TCEP, 1 mM inositol hexaphosphate (phytic acid) and 45 % pentaerythritol propoxylate (5/4 PO/OH)
Matthews coefficient: 2.3
Solvent content (%): 46.65
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: 2023-09-06
Human Sirt6 in complex with the inhibitor S6023 and ADP-ribose (PDB entry 8BL0)
Macromolecule: NAD-dependent protein deacetylase sirtuin-6
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.286
Sequence length: 302 residues
Sequence: GIDPFTADKGKCGLPEIFDPPEELERKVWELARLVWQSSSVVFHTGAGISTASGIPDFRGPHGVWTMEERGLAPKFDTTFESARPTQTHMALVQLERVGLLRFLVSQNVDGLHVRSGFPRDKLAELHGNMFVEECAKCKTQYVRDTVVGTMGLKATGRLCTVAKARGLRACRGELRDTILDWEDSLPDRDLALADEASRNADLSITLGTSLQIRPSGNLPLATKRRGGRLVIVNLQPTKHDRHADLRIHGYVDEVMTRLMKHLGLEIPAWDGPRVLERALPPLPRPPTPKLEPKEESPTRIN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.82
R work: 0.2014
R free: 0.2393
Average B factor: 40.314
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.7
Crystallization temperature (K): 293
Crystal growth procedure: 1.6 M (NH4)2SO4, 10% PEG 400, and Bis-Tris buffer pH 5.7
Matthews coefficient: 2.62
Solvent content (%): 53.01
Ligand: [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL
[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE (AR6)
Ligand formula: C15 H23 N5 O14 P2
Ligand molecular weight: 559.316
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)O)O)O)O)O)N
Ligand InChI: InChI=1S/C15H23N5O14P2/c16-12-7-13(18-3-17-12)20(4-19-7)14-10(23)8(21)5(32-14)1-30-35(26,27)34-36(28,29)31-2-6-9(22)11(24)15(25)33-6/h3-6,8-11,14-15,21-25H,1-2H2,(H,26,27)(H,28,29)(H2,16,17,18)/t5-,6-,8-,9-,10-,11-,14-,15+/m1/s1
Release date: 2023-11-22
INPP5D PanDDA analysis group deposition -- Crystal Structure of the phosphatase and C2 domains of SHIP1 in complex with Z2856434884 (PDB entry 5RX8)
Macromolecule: Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.86
Sequence length: 463 residues
Sequence: SMEQPEPDMITIFIGTWNMGNAPPPKKITSWFLSKGQGKTRDDSADYIPHDIYVIGTQEDPLSEKEWLEILKHSLQEITSVTFKTVAIHTLWNIRIVVLAKPEHENRISHICTDNVKTGIANTLGNKGAVGVSFMFNGTSLGFVNSHLTSGSEKKLRRNQNYMNILRFLALGDKKLSPFNITHRFTHLFWFGDLNYRVDLPTWEAETIIQKIKQQQYADLLSHDQLLTERREQKVFLHFEEEEITFAPTYRFERLTRDKYAYTKQKATGMKYNLPSWCDRVLWKSYPLVHVVCQSYGSTSDIMTSDHSPVFATFEAGVTSQFVSKNGPGTVDSQGQIEFLRCYATLKTKSQTKFYLEFHSSCLESFVKSQEGENEEGSEGELVVKFGETLPKLKPIISDPEYLLDQHILISIKSSDSDESYGEGCIALRLEATETQLPIYTPLTHHGELTGHFQGEIKLQTSQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.34
R work: 0.17
R free: 0.1937
Average B factor: 18.019
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 30 mM sodium nitrate, 30 mM dibasic sodium phosphate, 30 mM ammonium sulfate, 100 mM MES/imidazole, pH 6.5, 20% PEG500 MME, 10% PEG20000
Matthews coefficient: 2.09
Solvent content (%): 41.24
Ligand: 1-[4-(3-phenylpropyl)piperazin-1-yl]ethan-1-one (O3J)
Ligand formula: C15 H22 N2 O
Ligand molecular weight: 246.348
Ligand SMILES: CC(=O)N1CCN(CC1)CCCc2ccccc2
Ligand InChI: InChI=1S/C15H22N2O/c1-14(18)17-12-10-16(11-13-17)9-5-8-15-6-3-2-4-7-15/h2-4,6-7H,5,8-13H2,1H3
Release date: 2020-11-11
Factor VIIa in complex with the inhibitor (5R,11R)-11-[(1-amino-4-fluoroisoquinolin-6-yl)amino]-16-(cyclopropylsulfonyl)-7-(2,2-difluoroethoxy)-5,13-dimethyl-2,13-diazatricyclo[13.3.1.1~6,10~]icosa-1(19),6(20),7,9,15,17-hexaene-3,12-dione (PDB entry 5TQG)
Macromolecule: Factor VIIa (Heavy Chain)
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.21
Sequence length: 254 residues
Sequence: IVGGKVCPKGECPWQVLLLVNGAQLCGGTLINTIWVVSAAHCFDKIKNWRNLIAVLGEHDLSEHDGDEQSRRVAQVIIPSTYVPGTTNHDIALLRLHQPVVLTDHVVPLCLPERTFSERTLAFVRFSLVSGWGQLLDRGATALELMVLNVPRLMTQDCLQQSRKVGDSPNITEYMFCAGYSDGSKDSCKGDSGGPHATHYRGTWYLTGIVSWGQGCATVGHFGVYTRVSQYIEWLQKLMRSEPRPGVLLRAPFP
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.183
R free: 0.2041
Average B factor: 29.43
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 277
Crystal growth procedure: 100 mM MES, pH 6.0, 20 mM CACL2, 17.5%(W/V) PEG 6000
Matthews coefficient: 3.94
Solvent content (%): 68.75
Ligand: (5R,11R)-11-[(1-amino-4-fluoroisoquinolin-6-yl)amino]-16-(cyclopropylsulfonyl)-7-(2,2-difluoroethoxy)-5,13-dimethyl-2,13-diazatricyclo[13.3.1.1~6,10~]icosa-1(19),6(20),7,9,15,17-hexaene-3,12-dione (7KS)
Ligand formula: C34 H34 F3 N5 O5 S
Ligand molecular weight: 681.724
Ligand SMILES: CC1CC(=O)Nc2ccc(c(c2)CN(C(=O)C(c3ccc(c1c3)OCC(F)F)Nc4ccc5c(c4)c(cnc5N)F)C)S(=O)(=O)C6CC6
Ligand InChI: InChI=1S/C34H34F3N5O5S/c1-18-11-31(43)40-21-5-10-29(48(45,46)23-6-7-23)20(12-21)16-42(2)34(44)32(19-3-9-28(25(18)13-19)47-17-30(36)37)41-22-4-8-24-26(14-22)27(35)15-39-33(24)38/h3-5,8-10,12-15,18,23,30,32,41H,6-7,11,16-17H2,1-2H3,(H2,38,39)(H,40,43)/t18-,32-/m1/s1
Release date: 2017-02-01
Structure of human DNA polymerase beta complexed with T in the template base paired with incoming non-hydrolyzable GTP and MANGANESE (PDB entry 4PHP)
Macromolecule: DNA (5'-D(*CP*CP*GP*AP*CP*TP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
Type: DNA, polydeoxyribonucleotide
Source organism: synthetic construct
Sequence length: 16 residues
Sequence: CCGACTGCGCATCAGC
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.6
R work: 0.1813
R free: 0.2616
Average B factor: 21.53
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 14%?23% PEG3400, and 350 mM sodium acetate in 50 mM imidazole (pH 7.5)
Matthews coefficient: 2.28
Solvent content (%): 46.08
Ligand: MANGANESE (II) ION (MN)
Ligand formula: Mn
Ligand molecular weight: 54.938
Ligand SMILES: [Mn+2]
Ligand InChI: InChI=1S/Mn/q+2
Release date: 2015-05-06
Sulfonated Calpeptin is a promising drug candidate against SARS-CoV-2 infections (PDB entry 8C3D)
Macromolecule: Cathepsin K
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.22.38
Sequence length: 215 residues
Sequence: APDSVDYRKKGYVTPVKNQGQCGSCWAFSSVGALEGQLKKKTGKLLNLSPQNLVDCVSENDGCGGGYMTNAFQYVQKNRGIDSEDAYPYVGQEESCMYNPTGKAAKCRGYREIPEGNEKALKRAVARVGPVSVAIDASLTSFQFYSKGVYYDESCNSDNLNHAVLAVGYGIQKGNKHWIIKNSWGENWGNKGYILMARNKNNACGIANLASFPKM
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.1959
R free: 0.2268
Average B factor: 11.37
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 30 % PEG-3350, 0.2 M CaCL2
Matthews coefficient: 2.32
Solvent content (%): 46.98
Ligand: CALCIUM ION (CA)
Ligand formula: Ca
Ligand molecular weight: 40.078
Ligand SMILES: [Ca+2]
Ligand InChI: InChI=1S/Ca/q+2
Release date: 2023-09-27
Thrombin in complex with 4-(((1-((2S)-1-((2R)-2-(benzylsulfonylamino)- 3-phenyl-propanoyl)pyrrolidin-2-yl)-1-oxo-ethyl)amino)methyl) benzamidine (PDB entry 4UFD)
Macromolecule: THROMBIN HEAVY CHAIN
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.5
Sequence length: 258 residues
Sequence: IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQFG
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.429
R work: 0.1336
R free: 0.1587
Average B factor: 19.9
Crystallization pH: 7.5
Crystal growth procedure: SEE MATERIALS AND METHODS SECTION OF PUBLICATION, pH 7.5
Matthews coefficient: 2.46
Solvent content (%): 50.09
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: 2016-01-27
Three dimensional structure of human carbonic anhydrase II in complex with 5-[(4Chlorobenzyl)sulfanyl]thiophene-2-sulfonamide (PDB entry 5MJN)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 259 residues
Sequence: SHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.17
R work: 0.13989
R free: 0.17349
Average B factor: 16.697
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 9
Crystallization temperature (K): 294
Crystal growth procedure: 1,54 M  SODIUM CITRATE 60 MM TRIS- HCL, PH 9.0, PROTEIN 10 MG/ML 5-10 MM INHIBITOR (STOCK SOLUTION WAS 100 MM INHIBITOR DISSOLVED IN 100%             DIMETHYL SULFOXIDE) VAPOR DIFFUSION, SITTING DROP,                  
TEMPERATURE 294K,  TIME 2-5 DAYS
Matthews coefficient: 2.1
Solvent content (%): 42
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: 2017-12-06
PanDDA analysis group deposition -- Crystal Structure of ATAD2 in complex with DF849 (PDB entry 5QXR)
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: SMQEEDTFRELRIFLRNVTHRLAIDKRFRVFTKPVDPDEVPDYRTVIKEPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNPDRDPGDRLIRHRACALRDTAYAIIKEELDEDFEQLCEEIQESR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.66
R work: 0.1693
R free: 0.1916
Average B factor: 29.315
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 277
Crystal growth procedure: 1.6M Ammonium Sulfate, 0.1M bis-tris pH 5.5
Matthews coefficient: 4.2
Solvent content (%): 70.7
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: 2020-04-08
PKG II's Amino Terminal Cyclic Nucleotide Binding Domain (CNB-A) in a complex with cGMP (PDB entry 5C8W)
Macromolecule: cGMP-dependent protein kinase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.12
Sequence length: 143 residues
Sequence: GSNKPPEFSFEKARVRKDSSEKKLITDALNKNQFLKRLDPQQIKDMVECMYGRNYQQGSYIIKQGEPGNHIFVLAEGRLEVFQGEKLLSSIPMWTTFGELAILYNCTRTASVKAITNVKTWALDREVFQNIMRRTAQARDEQY
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.1621
R free: 0.1955
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5
Crystallization temperature (K): 293
Crystal growth procedure: 33 mM cGMP, 200 mM sodium malonate, 5-10% ethylene glycol, 20% PEG
Matthews coefficient: 2.14
Solvent content (%): 42.59
Ligand: MALONIC ACID (MLA)
Ligand formula: C3 H4 O4
Ligand molecular weight: 104.061
Ligand SMILES: C(C(=O)O)C(=O)O
Ligand InChI: InChI=1S/C3H4O4/c4-2(5)1-3(6)7/h1H2,(H,4,5)(H,6,7)
Release date: 2016-01-20
Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with T-48 (PDB entry 6NJH)
Macromolecule: cAMP-specific 3',5'-cyclic phosphodiesterase 4D
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.53
Sequence length: 370 residues
Sequence: MSIPRFGVKTEQEDVLAKELEDVNKWGLHVFRIAELSGNRPLTVIMHTIFQERDLLKTFKIPVDTLITYLMTLEDHYHADVAYHNNIHAADVVQSTHVLLSTPALEAVFTDLEILAAIFASAIHDVDHPGVSNQFLINTNSELALMYNDSSVLENHHLAVGFKLLQEENCDIFQNLTKKQRQSLRKMVIDIVLATDMSKHMNLLADLKTMVETKKVTSSGVLLLDNYSDRIQVLQNMVHCADLSNPTKPLQLYRQWTDRIMEEFFRQGDRERERGMEISPMCDKHNASVEKSQVGFIDYIVHPLWETWADLVHPDAQDILDTLEDNREWYQSTIPQAPAPPLDEQNRDSQGNQVSEFISNTFLDENLYFQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.15
R work: 0.172
R free: 0.21
Average B factor: 27.97
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 289
Crystal growth procedure: 4.6MG/ML VCID7620 + 0.5MM T-048-1
 1MM DTT, 0.1MM ZNCL2, 0.1MM MGCL2 (BATCH 1214013) AGAINST
 SPARSE MATRIX CONDITION MORPHEUS C4, 12.5% W/V PEG1,000 ,
 12.5% W/V PEG3,350 , 12.5% W/V MPD , 0.03M NPS (SODIUM
 NITRATE, DISODIUM HYDROGEN PHOSPHATE, AMMONIUM SULFATE), 0.1M
 MES/IMIDAZOLE PH 6.5, CRYO-PROTECTED - DIRECT (QYM9-2), VAPOR
 DIFFUSION, SITTING DROP, TEMPERATURE 289K
Matthews coefficient: 2.15
Solvent content (%): 42.89
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: 2019-05-08
HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with a Spiro[4.5]decanone inhibitor (JPHM-2-167) (PDB entry 6QGV)
Macromolecule: Egl nine homolog 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11.29
Sequence length: 233 residues
Sequence: GSHMASPNGQTKPLPALKLALEYIVPCMNKHGICVVDDFLGKETGQQIGDEVRALHDTGKFTDGQLVSQKSDSSKDIRGDKITWIEGKEPGCETIGLLMSSMDDLIRHCNGKLGSYKINGRTKAMVACYPGNGTGYVRHVDNPNGDGRCVTCIYYLNKDWDAKVSGGILRIFPEGKAQFADIEPKFDRLLFFWSDRRNPHEVQPAYATRYAITVWYFDADERARAKVKYLTGE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.4
R work: 0.1569
R free: 0.1722
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 2.0 M Ammonium sulfate, 5% v/v 2-propanol
Matthews coefficient: 2.19
Solvent content (%): 43.83
Ligand: MANGANESE (II) ION (MN)
Ligand formula: Mn
Ligand molecular weight: 54.938
Ligand SMILES: [Mn+2]
Ligand InChI: InChI=1S/Mn/q+2
Release date: 2020-02-05
Crystal Structure of Bruton's Tyrosine Kinase bound to a Cinnoline Fragment (PDB entry 4ZLY)
Macromolecule: Tyrosine-protein kinase BTK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 270 residues
Sequence: GLGYGSWEIDPKDLTFLKELGTGQFGVVKYGKWRGQYDVAIKMIKEGSMSEDEFIEEAKVMMNLSHEKLVQLYGVCTKQRPIFIITEYMANGCLLNYLREMRHRFQTQQLLEMCKDVCEAMEYLESKQFLHRDLAARNCLVNDQGVVKVSDFGLSRYVLDDEYTSSVGSKFPVRWSPPEVLMYSKFSSKSDIWAFGVLMWEIYSLGKMPYERFTNSETAEHIAQGLRLYRPHLASEKVYTIMYSCWHEKADERPTFKILLSNILDVMDEE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.65
R work: 0.163
R free: 0.1965
Average B factor: 16.117
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 277
Crystal growth procedure: 10% polyethylene glycol 4000, 20% glycerol, 0.1M imidazole/MES, pH 6.5, 0.12M alcohol mixture
Matthews coefficient: 2.3
Solvent content (%): 46.46
Ligand: IMIDAZOLE (IMD)
Ligand formula: C3 H5 N2
Ligand molecular weight: 69.085
Ligand SMILES: c1c[nH+]c[nH]1
Ligand InChI: InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5)/p+1
Release date: 2015-07-01
Crystal structure of KLK6 in complex with compound DKFZ917 (PDB entry 7QHZ)
Macromolecule: Kallikrein-6
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21
Sequence length: 223 residues
Sequence: LVHGGPCDKTSHPYQAALYTSGHLLCGGVLIHPLWVLTAAHCKKPNLQVFLGKHNLGQQESSQEQSSVVRAVIHPDYDAASHDQDIMLLRLARPAKLSELIQPLPLERDCSAQTTSCHILGWGKTADGDFPDTIQCAYIHLVSREECEHAYPGQITQNMLCAGDEKYGKDSCQGDSGGPLVCGDHLRGLVSWGNIPCGSKEKPGVYTNVCRYTNWIQKTIQAK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.5
R work: 0.1822
R free: 0.219
Average B factor: 21.0381
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 298
Crystal growth procedure: 0.20 M trimethylamine N-oxide, 0.1 M Tris-HCl pH8.5, 20% PEG MME 2000
Matthews coefficient: 2.38
Solvent content (%): 48.36
Ligand: (5~{R})-3-(4-carbamimidoylphenyl)-~{N}-[(1~{S})-1-naphthalen-1-ylpropyl]-2-oxidanylidene-1,3-oxazolidine-5-carboxamide (CI5)
Ligand formula: C24 H24 N4 O3
Ligand molecular weight: 416.472
Ligand SMILES: CCC(c1cccc2c1cccc2)NC(=O)C3CN(C(=O)O3)c4ccc(cc4)C(=N)N
Ligand InChI: InChI=1S/C24H24N4O3/c1-2-20(19-9-5-7-15-6-3-4-8-18(15)19)27-23(29)21-14-28(24(30)31-21)17-12-10-16(11-13-17)22(25)26/h3-13,20-21H,2,14H2,1H3,(H3,25,26)(H,27,29)/t20-,21+/m0/s1
Release date: 2022-11-23
Carbonic Anhydrase IX Mimic Complexed with N-(5-sulfamoyl-1,3,4-thiadiazol-2-yl)isobutyramide (PDB entry 7JO2)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 260 residues
Sequence: MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHSFQVTFDDSQDKAVLKGGPLDGTYRLLQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDVGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTEGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLAECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.307
R work: 0.1712
R free: 0.1905
Average B factor: 16.7907
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 1.6M Sodium Citrate, 50mM Tris
Matthews coefficient: 2.07
Solvent content (%): 40.55
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: 2020-11-04
Atrial Natriuretic Peptide Receptor complexed with deletion mutant of human Atrial Natriuretic Peptide[7-28] (PDB entry 7BRJ)
Macromolecule: Atrial natriuretic peptide receptor 1
Type: Protein, polypeptide(L)
Source organism: Rattus norvegicus
EC number: 4.6.1.2
Sequence length: 435 residues
Sequence: SDLTVAVVLPLTNTSYPWSWARVGPAVELALARVKARPDLLPGWTVRMVLGSSENAAGVCSDTAAPLAAVDLKWEHSPAVFLGPGCVYSAAPVGRFTAHWRVPLLTAGAPALGIGVKDEYALTTRTGPSHVKLGDFVTALHRRLGWEHQALVLYADRLGDDRPCFFIVEGLYMRVRERLNITVNHQEFVEGDPDHYPKLLRAVRRKGRVIYICSSPDAFRNLMLLALNAGLTGEDYVFFHLDVFGQSLKSAQGLVPQKPWERGDGQDRSARQAFQAAKIITYKEPDNPEYLEFLKQLKLLADKKFNFTVEDGLKNIIPASFHDGLLLYVQAVTETLAQGGTVTDGENITQRMWNRSFQGVTGYLKIDRNGDRDTDFSLWDMDPETGAFRVVLNYNGTSQELMAVSEHKLYWPLGYPPPDVPKCGFDNEDPACNQD
Oligomeric state: Hetero 3-mer
Stoichiometry: A2, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.7
R work: 0.1927
R free: 0.2335
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 300
Crystal growth procedure: Sodium malonate, MES
Matthews coefficient: 3.77
Solvent content (%): 67.38
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: 2021-03-31
Crystal structure of cysteine-bound ferrous form of the matured F2-Tyr157 human cysteine dioxygenase (PDB entry 6BPV)
Macromolecule: Cysteine dioxygenase type 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.13.11.20
Sequence length: 200 residues
Sequence: SEQTEVLKPRTLADLIRILHQLFAGDEVNVEEVQAIMEAYESDPTEWAMYAKFDQYRYTRNLVDQGNGKFNLMILCWGEGHGSSIHDHTNSHCFLKMLQGNLKETLFAWPDKKSNEMVKKSERVLRENQCAYINDSVGLHRVENISHTEPAVSLHLXSPPFDTCHAFDQRTGHKNKVTMTFHSKFGIRTPNATSGSLENN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.95
R work: 0.1604
R free: 0.1792
Average B factor: 34.2298
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 295
Crystal growth procedure: 0.1 M MES, 2 M ammonium sulfate, 2% PEG400
Matthews coefficient: 3.71
Solvent content (%): 66.83
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: 2018-07-04
JAK3 with Cyanamide CP34 (PDB entry 6DB4)
Macromolecule: Tyrosine-protein kinase JAK3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 321 residues
Sequence: MGHHHHHHQDPTIFEERHLKYISQLGKGNFGSVELCRYDPLGDNTGALVAVKQLQHSGPDQQRDFQREIQILKALHSDFIVKYRGVSYGPGRQSLRLVMEYLPSGCLRDFLQRHRARLDASRLLLYSSQICKGMEYLGSRRCVHRDLAARNILVESEAHVKIADFGLAKLLPLDKDYYVVREPGQSPIFWYAPESLSDNIFSRQSDVWSFGVVLYELFTYCDKSCSPSAEFLRMMGCERDVPALSRLLELLEEGQRLPAPPACPAEVHELMKLCWAPSPQDRPSFSALGPQLDMLWSGSRGCETHAFTAHPEGKHHSLSFS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.662
R work: 0.1852
R free: 0.2157
Average B factor: 32.52
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 298
Crystal growth procedure: 20% PEG 3350, 0.2M (NH4)2SO4, 2% phenylurea
Matthews coefficient: 2.19
Solvent content (%): 43.87
Ligand: N-[(1S)-6-(5-phenyl-7H-pyrrolo[2,3-d]pyrimidin-4-yl)-2,3-dihydro-1H-inden-1-yl]imidoformamide (G4Y)
Ligand formula: C22 H19 N5
Ligand molecular weight: 353.42
Ligand SMILES: c1ccc(cc1)c2c[nH]c3c2c(ncn3)c4ccc5c(c4)C(CC5)NC=N
Ligand InChI: InChI=1S/C22H19N5/c23-12-25-19-9-8-15-6-7-16(10-17(15)19)21-20-18(14-4-2-1-3-5-14)11-24-22(20)27-13-26-21/h1-7,10-13,19H,8-9H2,(H2,23,25)(H,24,26,27)/t19-/m0/s1
Release date: 2018-11-28
ASH1L SET domain S2259M mutant in complex with S-adenosyl methionine (SAM) (PDB entry 4YNP)
Macromolecule: Histone-lysine N-methyltransferase ASH1L
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.43
Sequence length: 226 residues
Sequence: GAMAGSYKKIRSNVYVDVKPLSGYEATTCNCKKPDDDTRKGCVDDCLNRMIFAECSPNTCPCGEQCCNQRIQRHEWVQCLERFRAEEKGWGIRTKEPLKAGQFIIEYLGEVVSEQEFRNRMIEQYHNHSDHYCLNLDSGMVIDSYRMGNEARFINHSCDPNCEMQKWSVNGVYRIGLYALKDMPAGTELTYDYNFHMFNVEKQQLCKCGFEKCRGIIGGKSQRVNG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.9
R work: 0.2619
R free: 0.3194
Average B factor: 54.671
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: PEG 3350, 20 mM Tris
Matthews coefficient: 2.39
Solvent content (%): 48.46
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: 2015-09-02