satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of SETDB1 Tudor domain with aryl triazole fragments (PDB entry 6AU3)
Macromolecule: Histone-lysine N-methyltransferase SETDB1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.43
Sequence length: 213 residues
Sequence: ENLYFQGDLIVSMRILGKKRTKTWHKGTLIAIQTVGPGKKYKVKFDNKGKSLLSGNHIAYDYHPPADKLYVGSRVVAKYKDGNQVWLYAGIVAETPNVKNKLRFLIFFDDGYASYVTQSELYPICRPLKKTWEDIEDISCRDFIEEYVTAYPNRPMVLLKSGQLIKTEWEGTWWKSRVEEVDGSLVRILFLDDKRCEWIYRGSTRLEPMFSMK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.1787
R free: 0.1903
Average B factor: 28.895
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 25% PEG3350, 0.2M LiSO4, 0.1M Bis-Tris pH 6.5
Matthews coefficient: 2.46
Solvent content (%): 50.08
Ligand: UNKNOWN ATOM OR ION (UNX)
Ligand formula: X
Ligand SMILES: *
Release date: 2017-09-27
Crystal structure of human Fanconi-associated nuclease 1 (PDB entry 4RY3)
Macromolecule: Fanconi-associated nuclease 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.21
Sequence length: 648 residues
Sequence: GHPYYLRSFLVVLKTVLENEDDMLLFDEQEKGIVTKFYQLSATGQKLYVRLFQRKLSWIKMTKLEYEEIALDLTPVIEELTNAGFLQTESELQELSEVLELLSAPELKSLAKTFHLVNPNGQKQQLVDAFLKLAKQRSVCTWGKNKPGIGAVILKRAKALAGQSVRICKGPRAVFSRILLLFSLTDSMEDEDAACGGQGQLSTVLLVNLGRMEFPSYTINRKTHIFQDRDDLIRYAAATHMLSDISSAMANGNWEEAKELAQCAKRDWNRLKNHPSLRCHEDLPLFLRCFTVGWIYTRILSRFVEILQRLHMYEEAVRELESLLSQRIYCPDSRGRWWDRLALNLHQHLKRLEPTIKCITEGLADPEVRTGHRLSLYQRAVRLRESPSCKKFKHLFQQLPEMAVQDVKHVTITGRLCPQRGMCKSVFVMEAGEAADPTTVLCSVEELALAHYRRSGFDQGIHGEGSTFSTLYGLLLWDIIFMDGIPDVFRNACQAFPLDLCTDSFFTSRRPALEARLQLIHDAPEESLRAWVAATWHEQEGRVASLVSWDRFTSLQQAQDLVSCLGGPVLSGVCRHLAADFRHCRGGLPDLVVWNSQSRHFKLVEVKGPNDRLSHKQMIWLAELQKLGAEVEVCHVVAVGGSENLYFQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.802
R work: 0.2078
R free: 0.2433
Average B factor: 48.9467
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.2
Crystallization temperature (K): 277
Crystal growth procedure: 2.5M sodium acetate, 0.1M Bis-Tris propane, 10% glycerol, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Matthews coefficient: 4.72
Solvent content (%): 73.92
Ligand: PLATINUM (II) ION (PT)
Ligand formula: Pt
Ligand molecular weight: 195.078
Ligand SMILES: [Pt+2]
Ligand InChI: InChI=1S/Pt/q+2
Release date: 2015-01-28
BACE2 xaperone complex with N-{3-[(5R)-3-amino-5-methyl-9,9-dioxo-2,9lambda6-dithia-4-azaspiro[5.5]undec-3-en-5-yl]-4-fluorophenyl}-5-(fluoromethoxy)pyrazine-2-carboxamide (PDB entry 6JSZ)
Macromolecule: Beta-secretase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.23.45
Sequence length: 386 residues
Sequence: ANFLAMVDNLQGDSGRGYYLEMLIGTPPQKLQILVDTGSSNFAVAGTPHSYIDTYFDTERSSTYRSKGFDVTVKYTQGSWTGFVGEDLVTIPKGFNTSFLVNIATIFESENFFLPGIKWNGILGLAYATLAKPSSSLETFFDSLVTQANIPNVFSMQMCGAGLPVAGSGTNGGSLVLGGIEPSLYKGDIWYTPIKEEWYYQIEILKLEIGGQSLNLDCREYNADKAIVDSGTTLLRLPQKVFDAVVEAVARASLIPEFSDGFWTGSQLACWTNSETPWSYFPKISIYLRDENSSRSFRITILPQLYIQPMMGAGLNYECYRFGISPSTNALVIGATVMEGFYVIFDRAQKRVGFAASPCAEIAGAAVSEISGPFSTEDVASNCVPA
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.53
R work: 0.2252
R free: 0.237
Average B factor: 28.96
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8
Crystallization temperature (K): 293.15
Crystal growth procedure: 0.1M TRIS pH 8.0, 25% PEG 3350, pH 8.0
Matthews coefficient: 2.31
Solvent content (%): 46.76
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: 2019-08-28
Structure of the catalytic domain of PPM1D/Wip1 serine/threonine phosphatase (PDB entry 8T2J)
Macromolecule: Protein phosphatase 1D
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.16
Sequence length: 345 residues
Sequence: MAGLYSLRVSVFSDQGGRKYMEDVTQIVVEPEETAERSSVAFFAVCDGHGGREAAQFAREHLWGFIKKQKGFTSSEPAKVCAAIRKGFLACHLAMWKKLAEWPKTMTGLPSTSGTTASVVIIRGMKMYVAHVGDSGVVLGIQDDPKDDFVRAVEVTQDHKPELPKERERIEGLGGSVMNKSGVNRVVWKRPALTHNGPVAASTVIDQIPFLAVARALGDLWSYDFFSGEFVVSPEPDTSVHTLDPQKHKYIILGSDGLWNMIPPQDAISMCQDQEEKKYLMGEHGQSCAKMLVNRALGRWRQRMLRADNTSAIVICISPEVDNQGNFTNEDELYLNLTDSPSYNS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.1747
R free: 0.2192
Average B factor: 37.69
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 298
Crystal growth procedure: 100 mM HEPES pH 7.5, 10% (w/v) PEG 3000, 20% PEG 400 (v/v), and 10% glycerol (v/v)
Matthews coefficient: 1.9
Solvent content (%): 35.3
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: 2024-06-12
Crystal Structure of POMGNT2 in complex with UDP and mono-mannosyl peptide (379Man short peptide) (PDB entry 7E9L)
Macromolecule: Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2
Type: Protein, polypeptide(L)
Source organism: Bos taurus
EC number: 2.4.1.312
Sequence length: 539 residues
Sequence: GAPPAPALRIDYPKALQILTEGGTHMVCTGRTHTDRLCRFKWLCYSSEAEEFIFFHGNASVMLPSLGSRRFQPALLDLSTVEDHNTQYFNFVELPAAALRFMPKPVFVPDVALIANRFNPDNLMHVFHDDLLPLFYTLRQFPGLAREARLFFMEGWGEGAHFDLYKLLSPKQPLLRAQLKALGRLLCFSHAFVGLSKVTTWYQYGFVQPQGPKANILVSGNEIRQFAHFLMEKLNVSQAGGPLGEEYILVFSRTQNRLILNEAELLLALAQEFQMKTVTVSLEDHAFADVVRLVSNASMLVSMHGAQLVTALFLPRGAAVVELFPYAVNPDHYTPYKTLATLPGMDLQYIAWQNTMPENTVTHPERPWDQGGIAHLDRAEQARILQSREVPRHLCCRNPEWLFRIYQDTKVDIPSLIQTIRRVVKGHPGPRKQKWTVSLYPGKVREARCQASVQGASEARLSVSWQIPWNLKYLKVREVKYEVWLQEQGENTYVPYMLALQNHTFTENIKPFTTYLVWIRCIFNKTLLGPFADVLVCST
Oligomeric state: Hetero 3-mer
Stoichiometry: A2, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.1855
R free: 0.2338
Average B factor: 50.08
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M Tris-HCl (pH 8.0 or 8.5), 12-16% PEG 8000, 1% tacsimate (pH 7.0)
Matthews coefficient: 2.46
Solvent content (%): 49.9
Ligand: alpha-D-mannopyranose (MAN)
Ligand formula: C6 H12 O6
Ligand molecular weight: 180.156
Ligand SMILES: C(C1C(C(C(C(O1)O)O)O)O)O
Ligand InChI: InChI=1S/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H2/t2-,3-,4+,5+,6+/m1/s1
Release date: 2021-05-05
Crystal structure of RhoA mutant L69R complexed with GDP (PDB entry 8GI6)
Macromolecule: Transforming protein RhoA
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 196 residues
Sequence: GPLMAAIRKKLVIVGDGACGKTCLLIVFSKDQFPEVYVPTVFENYVADIEVDGKQVELALWDTAGQEDYDRRRPLSYPDTDVILMCFSIDSPDSLENIPEKWTPEVKHFCPNVPIILVGNKKDLRNDEHTRRELAKMKQEPVKPEEGRDMANRIGAFGYMECSAKTKDGVREVFEMATRAALQARRGKKKSGCLVL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.4
R work: 0.15306
R free: 0.18173
Average B factor: 12.222
Crystallization method: MICROBATCH
Crystallization pH: 5.7
Crystallization temperature (K): 293.15
Crystal growth procedure: 0.1 M Na acetate (pH 5.7), 0.5 mM Na citrate, 26% PEG4000, 5% glycerol
Matthews coefficient: 2.04
Solvent content (%): 39.68
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: 2024-03-20
Binary complex crystal structure of DNA polymerase Beta with T:G mismatch at the primer terminus (PDB entry 5J0X)
Macromolecule: DNA polymerase beta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 335 residues
Sequence: MSKRKAPQETLNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPSAARKFVDEGIKTLEDLRKNEDKLNHHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSESTKQPKLLHQVVEQLQKVHFITDTLSKGETKFMGVCQLPSKNDEKEYPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGEPLPVDSEKDIFDYIQWKYREPKDRSE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.1931
R free: 0.2417
Average B factor: 25.6852
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 16-18% PEG 3350, 50 mM Imidazole, 350 mM Sodium Acetate
Matthews coefficient: 2.42
Solvent content (%): 49.07
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2016-10-26
Structure of human DNA polymerase beta complexed with 8-ClG in the template base paired with incoming non-hydrolyzable GTP (PDB entry 6CRH)
Macromolecule: DNA polymerase beta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 335 residues
Sequence: MSKRKAPQETLNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPSAARKFVDEGIKTLEDLRKNEDKLNHHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSESTKQPKLLHQVVEQLQKVHFITDTLSKGETKFMGVCQLPSKNDEKEYPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGEPLPVDSEKDIFDYIQWKYREPKDRSE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.327
R work: 0.1974
R free: 0.2438
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 14% to 23% PEG3400, and 350 mM sodium acetate in 50 mM imidazole (pH 7.5)
Matthews coefficient: 2.4
Solvent content (%): 48.7
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: 2019-03-20
Structural basis for inhibition of human autotaxin by four novel compounds (PDB entry 4ZG6)
Macromolecule: Ectonucleotide pyrophosphatase/phosphodiesterase family member 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.39
Sequence length: 855 residues
Sequence: TFAVGVNICLGFTAHRIKRAEGWEEGPPTVLSDSPWTNISGSCKGRCFELQEAGPPDCRCDNLCKSYTSCCHDFDELCLKTARGWECTKDRCGEVRNEENACHCSEDCLARGDCCTNYQVVCKGESHWVDDDCEEIKAAECPAGFVRPPLIIFSVDGFRASYMKKGSKVMPNIEKLRSCGTHSPYMRPVYPTKTFPNLYTLATGLYPESHGIVGNSMYDPVFDATFHLRGREKFNHRWWGGQPLWITATKQGVKAGTFFWSVVIPHERRILTILQWLTLPDHERPSVYAFYSEQPDFSGHKYGPFGPEMTNPLREIDKIVGQLMDGLKQLKLHRCVNVIFVGDHGMEDVTCDRTEFLSNYLTNVDDITLVPGTLGRIRSKFSNNAKYDPKAIIAALTCKKPDQHFKPYLKQHLPKRLHYANNRRIEDIHLLVERRWHVARKPLDVYKKPSGKCFFQGDHGFDNKVNSMQTVFVGYGSTFKYKTKVPPFENIELYNVMCDLLGLKPAPNNGTHGSLNHLLRTNTFRPTMPEEVTRPNYPGIMYLQSDFDLGCTCDDKVEPKNKLDELNKRLHTKGSTEERHLLYGRPAVLYRTRYDILYHTDFESGYSEIFLMPLWTSYTVSKQAEVSSVPDHLTSCVRPDVRVSPSFSQNCLAYKNDKQMSYGFLFPPYLSSSPEAKYDAFLVTNMVPMYPAFKRVWNYFQRVLVKKYASERNGVNVISGPIFDYDYDGLHDTEDKIKQYVEGSSIPVPTHYYSIITSCLDFTQPADKCDGPLSVSSFILPHRPDNEESCNSSEDESKWVEELMKMHTARVRDIEHLTSLDFFRKTSRSYPEILTLKTYLHTYESEIHHHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.22039
R free: 0.265
Average B factor: 37.642
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 20% PEG 3350, 0.4 M NaSCN
Matthews coefficient: 2.42
Solvent content (%): 49.2
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: 2015-10-14
DNA polymerase beta substrate complex with templating cytosine and incoming Fapy-dGTP analog (PDB entry 6DIA)
Macromolecule: DNA polymerase beta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 335 residues
Sequence: MSKRKAPQETLNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPSAARKFVDEGIKTLEDLRKNEDKLNHHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSESTKQPKLLHQVVEQLQKVHFITDTLSKGETKFMGVCQLPSKNDEKEYPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGEPLPVDSEKDIFDYIQWKYREPKDRSE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.969
R work: 0.1964
R free: 0.2462
Average B factor: 32.6009
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8
Crystallization temperature (K): 291
Crystal growth procedure: 50 mM imidazole, 350 mM sodium chloride, 15% PEG3350, pH 8.0
Matthews coefficient: 2.5
Solvent content (%): 50.83
Ligand: 1-[2-amino-5-(formylamino)-6-oxo-1,6-dihydropyrimidin-4-yl]-2,5-anhydro-1,3-dideoxy-6-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-D-ribo-hexitol (GKS)
Ligand formula: C11 H19 N4 O14 P3
Ligand molecular weight: 524.208
Ligand SMILES: C1C(OC(C1O)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)CC2=C(C(=O)NC(=N2)N)NC=O
Ligand InChI: InChI=1S/C11H19N4O14P3/c12-11-14-6(9(13-4-16)10(18)15-11)1-5-2-7(17)8(27-5)3-26-31(22,23)29-32(24,25)28-30(19,20)21/h4-5,7-8,17H,1-3H2,(H,13,16)(H,22,23)(H,24,25)(H2,19,20,21)(H3,12,14,15,18)/t5-,7-,8+/m0/s1
Release date: 2019-01-30
Crystal Structure of KRAS G12D with compound 24 (4-(4-[(1R,5S)-3,8-diazabicyclo[3.2.1]octan-3-yl]-8-fluoro-2-{[(2S,4S,7aR)-2-fluorotetrahydro-1H-pyrrolizin-7a(5H)-yl]methoxy}pyrido[4,3-d]pyrimidin-7-yl)naphthalen-2-ol) bound (PDB entry 7RT3)
Macromolecule: Isoform 2B of GTPase KRas
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 170 residues
Sequence: GMTEYKLVVVGADGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETSLLDILDTAGQEEYSAMRDQYMRTGEGFLLVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKSDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.56
R work: 0.1642
R free: 0.1988
Average B factor: 21.5202
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 298
Crystal growth procedure: 28% PEG8000, 100 mM sodium citrate, pH 4.6, 100 mM ammonium acetate
Matthews coefficient: 2.46
Solvent content (%): 50.05
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: 2021-12-22
Crystal structure of the Pri1 subunit of human primase bound to 2F-ATP (PDB entry 6R5E)
Macromolecule: DNA primase small subunit
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7
Sequence length: 410 residues
Sequence: GTSMETFDPTELPELLKLYYRRLFPYSQYYRWLNYGGVIKNYFQHREFSFTLKDDIYIRYQSFNNQSDLEKEMQKMNPYKIDIGAVYSHRPNQHNTVKLGAFQAQEKELVFDIDMTDYDDVRRCCSSADICPKCWTLMTMAIRIIDRALKEDFGFKHRLWVYSGRRGVHCWVCDESVRKLSSAVRSGIVEYLSLVKGGQDVKKKVHLSEKIHPFIRKSINIIKKYFEEYALVNQDILENKESWDKILALVPETIHDELQQSFQKSHNSLQRWEHLKKVASRYQNNIKNDKYGPWLEWEIMLQYCFPRLDINVSKGINHLLKSPFSVHPKTGRISVPIDLQKVDQFDPFTVPTISFICRELDAISTNEEEKEENEAESDVKHRTRDYKKTSLAPYVKVFEHFLENLDKSRK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.85
R work: 0.1784
R free: 0.2057
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 292
Crystal growth procedure: 23% PEG3350, 10% ethylene glycol, 200 mM Na/K tartrate
Matthews coefficient: 2.52
Solvent content (%): 51.26
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: 2019-09-11
Complex of PKA with the bisubstrate protein kinase inhibitor ARC-1408 (PDB entry 5IZF)
Macromolecule: cAMP-dependent protein kinase catalytic subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.11
Sequence length: 351 residues
Sequence: MGNAAAAKKGSEQESVKEFLAKAKEDFLKKWESPAQNTAHLDQFERIKTLGTGSFGRVMLVKHKETGNHYAMKILDKQKVVKLKQIEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLYMVMEYVPGGEMFSHLRRIGRFSEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLLIDQQGYIQVTDFGFAKRVKGRTWTLCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKVRFPSHFSSDLKDLLRNLLQVDLTKRFGNLKNGVNDIKNHKWFATTDWIAIYQRKVEAPFIPKFKGPGDTSNFDDYEEEEIRVSINEKCGKEFSEF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.23
R free: 0.27
Average B factor: 63.48
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 277.15
Crystal growth procedure: 0.1M BisTris pH7.0, 0.2M amminium sulfate, 20%-24% PEG 3350
Matthews coefficient: 2.65
Solvent content (%): 53.6
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: 2016-07-20
Theophylline-Notum complex (PDB entry 6TUZ)
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): 1.24
R work: 0.2013
R free: 0.2167
Average B factor: 21.2903
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 4.2
Crystallization temperature (K): 300
Crystal growth procedure: 1.5 M Ammonium sulphate
0.1 M sodium citrate pH4.2
Matthews coefficient: 2
Solvent content (%): 38.51
Ligand: DIMETHYL SULFOXIDE (DMS)
Ligand formula: C2 H6 O S
Ligand molecular weight: 78.133
Ligand SMILES: CS(=O)C
Ligand InChI: InChI=1S/C2H6OS/c1-4(2)3/h1-2H3
Release date: 2020-10-28
STRUCTURE OF THE WNT DEACYLASE NOTUM - CRYSTAL FORM II - 2.8A (PDB entry 4UYZ)
Macromolecule: PROTEIN NOTUM HOMOLOG
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.1.1
Sequence length: 471 residues
Sequence: ETGRTEAAPAAGQPVESFPLDFTAVEGNMDSFMAQVKSLAQSLYPCSAQQLNEDLRLHLLLNTSVTCNDGSPAGYYLKESRGSRRWLLFLEGGWYCFNRENCDSRYDTMRRLMSSRDWPRTRTGTGILSSQPEENPYWWNANMVFIPYCSSDVWSGASSKSEKNEYAFMGALIIQEVVRELLGRGLSGAKVLLLAGSSAGGTGVLLNVDRVAEQLEKLGYPAIQVRGLADSGWFLDNKQYRHTDCVDTITCAPTEAIRRGIRYWNGVVPERCRRQFQEGEEWNCFFGYKVYPTLRCPVFVVQWLFDEAQLTVDNVHLTGQPVQEGLRLYIQNLGRELRHTLKDVPASFAPACLSHEIIIRSHWTDVQVKGTSLPRALHCWDRSLHDSHKASKTPLKGCPVHLVDSCPWPHCNPSCPTVRDQFTGQEMNVAQFLMHMGFDMQTVAQPQGLEPSELLGMLSNGSGTKHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.8
R work: 0.24761
R free: 0.29294
Average B factor: 46.978
Crystallization pH: 6
Crystal growth procedure: pH 6.0
Matthews coefficient: 2.09
Solvent content (%): 41.26
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: 2015-02-25
Crystal structure of the Pri1 subunit of human primase bound to fludarabine triphosphate (PDB entry 6R4U)
Macromolecule: DNA primase small subunit
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7
Sequence length: 410 residues
Sequence: GTSMETFDPTELPELLKLYYRRLFPYSQYYRWLNYGGVIKNYFQHREFSFTLKDDIYIRYQSFNNQSDLEKEMQKMNPYKIDIGAVYSHRPNQHNTVKLGAFQAQEKELVFDIDMTDYDDVRRCCSSADICPKCWTLMTMAIRIIDRALKEDFGFKHRLWVYSGRRGVHCWVCDESVRKLSSAVRSGIVEYLSLVKGGQDVKKKVHLSEKIHPFIRKSINIIKKYFEEYALVNQDILENKESWDKILALVPETIHDELQQSFQKSHNSLQRWEHLKKVASRYQNNIKNDKYGPWLEWEIMLQYCFPRLDINVSKGINHLLKSPFSVHPKTGRISVPIDLQKVDQFDPFTVPTISFICRELDAISTNEEEKEENEAESDVKHRTRDYKKTSLAPYVKVFEHFLENLDKSRK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.1961
R free: 0.2232
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 292
Crystal growth procedure: 23% PEG3350, 10% ethylene glycol, 200 mM Na/K tartrate
Matthews coefficient: 2.49
Solvent content (%): 50.55
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: 2019-09-11
Crystal Structure of Human Kallikrein 6 (I218Y) in complex with GSK3397892A (PDB entry 6SKD)
Macromolecule: Kallikrein-6
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21
Sequence length: 223 residues
Sequence: LVHGGPCDKTSHPYQAALYTSGHLLCGGVLIHPLWVLTAAHCKKPNLQVFLGKHNLGQQESSQEQSSVVRAVIHPDYDAASHDQDIMLLRLARPAKLSELIQPLPLERDCSAQTTSCHILGWGKTADGDFPDTIQCAYIHLVSREECEHAYPGQITQNMLCAGDEKYGKDSCQGDSGGPLVCGDHLRGLVSWGNYPCGSKEKPGVYTNVCRYTNWIQKTIQAK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.26
R work: 0.224
R free: 0.282
Average B factor: 43.63
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.6
Crystallization temperature (K): 293
Crystal growth procedure: 100mM Tris-HCl pH 8.6, PEG 4000 18-28%
Matthews coefficient: 2.18
Solvent content (%): 43.6
Ligand: UNKNOWN ATOM OR ION (UNX)
Ligand formula: X
Ligand SMILES: *
Release date: 2019-09-25
Crystal structure of human PI3K-gamma in complex with quinoline-containing inhibitor 5g (PDB entry 5KAE)
Macromolecule: Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.1.153
Sequence length: 959 residues
Sequence: SEESQAFQRQLTALIGYDVTDVSNVHDDELEFTRRGLVTPRMAEVASRDPKLYAMHPWVTSKPLPEYLWKKIANNCIFIVIHRSTTSQTIKVSPDDTPGAILQSFFTKMAKKKSLMDIPESQSEQDFVLRVCGRDEYLVGETPIKNFQWVRHCLKNGEEIHVVLDTPPDPALDEVRKEEWPLVDDCTGVTGYHEQLTIHGKDHESVFTVSLWDCDRKFRVKIRGIDIPVLPRNTDLTVFVEANIQHGQQVLCQRRTSPKPFTEEVLWNVWLEFSIKIKDLPKGALLNLQIYCGKAPALSSKASAESPSSESKGKVQLLYYVNLLLIDHRFLLRRGEYVLHMWQISGKGEDQGSFNADKLTSATNPDKENSMSISILLDNYCHPIALPKHQPTPDPEGDRVRAEMPNQLRKQLEAIIATDPLNPLTAEDKELLWHFRYESLKHPKAYPKLFSSVKWGQQEIVAKTYQLLARREVWDQSALDVGLTMQLLDCNFSDENVRAIAVQKLESLEDDDVLHYLLQLVQAVKFEPYHDSALARFLLKRGLRNKRIGHFLFWFLRSEIAQSRHYQQRFAVILEAYLRGCGTAMLHDFTQQVQVIEMLQKVTLDIKSLSAEKYDVSSQVISQLKQKLENLQNSQLPESFRVPYDPGLKAGALAIEKCKVMASKKKPLWLEFKCADPTALSNETIGIIFKHGDDLRQDMLILQILRIMESIWETESLDLCLLPYGCISTGDKIGMIEIVKDATTIAKIQQSTVGNTGAFKDEVLNHWLKEKSPTEEKFQAAVERFVYSCAGYCVATFVLGIGDRHNDNIMITETGNLFHIDFGHILGNYKSFLGINKERVPFVLTPDFLFVMGTSGKKTSPHFQKFQDICVKAYLALRHHTNLLIILFSMMLMTGMPQLTSKEDIEYIRDALTVGKNEEDAKKYFLDQIEVCRDKGWTVQFNWFLHLVLGIKQGEKHSA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.65
R work: 0.2007
R free: 0.2519
Average B factor: 66.35
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7.3
Crystallization temperature (K): 298
Crystal growth procedure: 20% PEG 3350, 250 mM ammonium sulfate, 100 mM Tris (pH 7.3), 2 mM dithiothreitol
Matthews coefficient: 2.34
Solvent content (%): 47.45
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: 2017-06-21