satarupa22/MacromolecularLigandDB huggingface dataset:
Death-associated Protein Kinase 1 (DAPK1) catalytic and auto-regulatory domains with S289A and S308E mutations (PDB entry 6FHB)
Macromolecule: Death-associated protein kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 337 residues
Sequence: GPMATVFRQENVDDYYDTGEELGSGQFAVVKKCREKSTGLQYAAKFIKKRRTKSSRRGVSREDIEREVSILKEIQHPNVITLHEVYENKTDVILILELVAGGELFDFLAEKESLTEEEATEFLKQILNGVYYLHSLQIAHFDLKPENIMLLDRNVPKPRIKIIDFGLAHKIDFGNEFKNIFGTPEFVAPEIVNYEPLGLEADMWSIGVITYILLSGASPFLGDTKQETLANVSAVNYEFEDEYFSNTSALAKDFIRRLLVKDPKKRMTIQDSLQHPWIKPKDTQQALSRKAAAVNMEKFKKFAARKKWKQEVRLISLCQRLSRSFLSRSNMSVARSD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.75
R work: 0.187
R free: 0.2215
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 292.15
Crystal growth procedure: 10% PEG 8000, 0.2M magnesium acetate
Matthews coefficient: 2.93
Solvent content (%): 57.99
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: 2019-01-30
Protein Tyrosine Phosphatase 1B F135Y mutant (PDB entry 6CWU)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 329 residues
Sequence: MEMEKEFEQIDKSGSWAAIYQDIRHEASDFPCRVAKLPKNKNRNRYRDVSPFDHSRIKLHQEDNDYINASLIKMEEAQRSYILTQGPLPNTCGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQKEEKEMIYEDTNLKLTLISEDIKSYYTVRQLELENLTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRESGSLSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKDPSSVDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFIMGDSSVQDQWKELSHEDLEPPPEHIPPPPRPPKRILEPHNLEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.08
R work: 0.25472
R free: 0.29122
Average B factor: 45.536
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277.15
Crystal growth procedure: 100 mM HEPES, 200 mM magnesium acetate, and 14% polyethylene glycol 8000, pH 7.5
Matthews coefficient: 3.16
Solvent content (%): 66.81
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: 2018-10-31
Crystal Structure of CK2alpha with N-(3-(((2-chloro-[1,1'-biphenyl]-4-yl)methyl)amino)propyl)methanesulfonamide bound (PDB entry 5MO7)
Macromolecule: Casein kinase II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 352 residues
Sequence: GSMDIEFDDDADDDGSGSGSGSGSSGPVPSRARVYTDVNTHRPSEYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.15
R work: 0.1894
R free: 0.2235
Average B factor: 64.71
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 298
Crystal growth procedure: 112.5mM Mes pH 6.5, 35% glycerol ethoxylate, 180 mM ammonium acetate
Matthews coefficient: 2.22
Solvent content (%): 44.56
Ligand: PHOSPHATE ION (PO4)
Ligand formula: O4 P
Ligand molecular weight: 94.971
Ligand SMILES: [O-]P(=O)([O-])[O-]
Ligand InChI: InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)/p-3
Release date: 2017-05-24
Crystal structure of BACE1 in complex with 2-aminooxazoline 3-aza-4-fluoro-xanthene inhibitor 22 (PDB entry 4WTU)
Macromolecule: Beta-secretase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.23.46
Sequence length: 411 residues
Sequence: LPRETDEEPEEPGKKGSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYNIPQTDES
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.85
R work: 0.1693
R free: 0.1957
Average B factor: 26.24
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.6
Crystallization temperature (K): 298
Crystal growth procedure: 21% PEG 5000 MME, 190 mM sodium citrate, 200 mM ammonium iodide
Matthews coefficient: 2.81
Solvent content (%): 56.27
Ligand: IODIDE ION (IOD)
Ligand formula: I
Ligand molecular weight: 126.904
Ligand SMILES: [I-]
Ligand InChI: InChI=1S/HI/h1H/p-1
Release date: 2015-03-04
Montbretin A analogue M06-MbA in complex with Human pancreatic alpha-amylase (PDB entry 6OCN)
Macromolecule: Pancreatic alpha-amylase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.1.1
Sequence length: 496 residues
Sequence: QYSPNTQQGRTSIVHLFEWRWVDIALECERYLAPKGFGGVQVSPPNENVAIYNPFRPWWERYQPVSYKLCTRSGNEDEFRNMVTRCNNVGVRIYVDAVINHMCGNAVSAGTSSTCGSYFNPGSRDFPAVPYSGWDFNDGKCKTGSGDIENYNDATQVRDCRLTGLLDLALEKDYVRSKIAEYMNHLIDIGVAGFRLDASKHMWPGDIKAILDKLHNLNSNWFPAGSKPFIYQEVIDLGGEPIKSSDYFGNGRVTEFKYGAKLGTVIRKWNGEKMSYLKNWGEGWGFVPSDRALVFVDNHDNQRGHGAGGASILTFWDARLYKMAVGFMLAHPYGFTRVMSSYRWPRQFQNGNDVNDWVGPPNNNGVIKEVTINPDTTCGNDWVCEHRWRQIRNMVIFRNVVDGQPFTNWYDNGSNQVAFGRGNRGFIVFNNDDWSFSLTLQTGLPAGTYCDVISGDKINGNCTGIKIYVSDDGKAHFSISNSAEDPFIAIHAESKL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.147
R work: 0.0988
R free: 0.1166
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 100 mM sodium cacodylate, 52-58% MPD
Matthews coefficient: 2.07
Solvent content (%): 40.53
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: 2020-02-12
Crystal structure of human NAMPT with fragment 5: (3E)-3-[(phenylamino)methylidene]oxan-2-one (PDB entry 5WI1)
Macromolecule: Nicotinamide phosphoribosyltransferase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.2.12
Sequence length: 491 residues
Sequence: MNPAAEAEFNILLATDSYKVTHYKQYPPNTSKVYSYFECREKKTENSKLRKVKYEETVFYGLQYILNKYLKGKVVTKEKIQEAKDVYKEHFQDDVFNEKGWNYILEKYDGHLPIEIKAVPEGFVIPRGNVLFTVENTDPECYWLTNWIETILVQSWYPITVATNSREQKKILAKYLLETSGNLDGLEYKLHDFGYRGVSSQETAGIGASAHLVNFKGTDTVAGLALIKKYYGTKDPVPGYSVPAAEHSTITAWGKDHEKDAFEHIVTQFSSVPVSVVSDSYDIYNACEKIWGEDLRHLIVSRSTQAPLIIRPDSGNPLDTVLKVLEILGKKFPVTENSKGYKLLPPYLRVIQGDGVDINTLQEIVEGMKQKMWSIENIAFGSGGGLLQKLTRDLLNCSFKCSYVVTNGLGINVFKDPVADPNKRSKKGRLSLHRTPAGNFVTLEEGKGDLEEYGQDLLHTVFKNGKVTKSYSFDEIRKNAQLNIELEAAHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.99
R work: 0.189
R free: 0.227
Average B factor: 20.89
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 277
Crystal growth procedure: PEG 10K, sodium chloride, glycerol, Tris
Matthews coefficient: 2.39
Solvent content (%): 48.63
Ligand: (3E)-3-[(phenylamino)methylidene]oxan-2-one (AOY)
Ligand formula: C12 H13 N O2
Ligand molecular weight: 203.237
Ligand SMILES: c1ccc(cc1)NC=C2CCCOC2=O
Ligand InChI: InChI=1S/C12H13NO2/c14-12-10(5-4-8-15-12)9-13-11-6-2-1-3-7-11/h1-3,6-7,9,13H,4-5,8H2/b10-9+
Release date: 2018-01-10
Crystal structure of CaMKII-actinin complex bound to AMPPNP (PDB entry 7B56)
Macromolecule: Calcium/calmodulin-dependent protein kinase type II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Mus musculus
EC number: 2.7.11.17
Sequence length: 317 residues
Sequence: SMMATITCTRFTEEYQLFEELGKGAFSVVRRCVKVLAGQEYAAKIINTKKLSARDHQKLEREARICRLLKHPNIVRLHDSISEEGHHYLIFDLVTGGELFEDIVAREYYSEADASHCIQQILEAVLHCHQMGVVHRDLKPENLLLASKLKGAAVKLADFGLAIEVEGEQQAWFGFAGTPGYLSPEVLRKDPYGKPVDLWACGVILYILLVGYPPFWDEDQHRLYQQIKAGAYDFPSPEWDTVTPEAKDLINKMLTINPSKRITAAEALKHPWISHRSTVASCMHRQETVDCLKKFNARRKLKGAILAAMLATRNFSG
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.45
R work: 0.1901
R free: 0.2154
Average B factor: 30.22
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M MES pH 6.0, 20% w/v PEG4000, 0.2 M Lithium Sulfate
Matthews coefficient: 2.45
Solvent content (%): 49.85
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: 2022-06-22
PanDDA analysis group deposition -- Crystal Structure of DCP2 (NUDT20) in complex with Z1203490773 (PDB entry 5QOR)
Macromolecule: DCP2 (NUDT20)
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.62
Sequence length: 167 residues
Sequence: SMGVPTYGAIILDETLENVLLVQGYLAKSGWGFPKGKVNKEEAPHDCAAREVFEETGFDIKDYICKDDYIELRINDQLARLYIIPGIPKDTKFNPKTRREIRNIEWFSIEKLPCHRNDMTPKSKLGLAPNKFFMAIPFIRPLRDWLSRRFGDSSDSDNGFSSTGSTP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.95
R work: 0.1958
R free: 0.2497
Average B factor: 40.788
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 4.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M acetate, pH 4.5, 5-25% PEG3350
Matthews coefficient: 2.5
Solvent content (%): 50.8
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: 2019-05-08
Crystal structure of human Pim-1 kinase in complex with a consensus peptide and fragment like molecule (E)-4-(4-hydroxyphenyl)but-3-en-2-one (PDB entry 5N4Z)
Macromolecule: Serine/threonine-protein kinase pim-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 313 residues
Sequence: MLLSKINSLAHLRAAPCNDLHATKLAPGKEKEPLESQYQVGPLLGSGGFGSVYSGIRVSDNLPVAIKHVEKDRISDWGELPNGTRVPMEVVLLKKVSSGFSGVIRLLDWFERPDSFVLILERPEPVQDLFDFITERGALQEELARSFFWQVLEAVRHCHNCGVLHRDIKDENILIDLNRGELKLIDFGSGALLKDTVYTDFDGTRVYSPPEWIRYHRYHGRSAAVWSLGILLYDMVCGDIPFEHDEEIIGGQVFFRQRVSSECQHLIRWCLALRPSDRPTFEEIQNHPWMQDVLLPQETAEIHLHSLSPGPSK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.257
R work: 0.1789
R free: 0.2077
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 277
Crystal growth procedure: HEPES
LiCl
Glycerol
DTT
BIS-TRIS-propane
PEG3350
Ethylene-glycol
DMSO
Matthews coefficient: 3.15
Solvent content (%): 61
Ligand: (~{E})-4-(4-hydroxyphenyl)but-3-en-2-one (8MK)
Ligand formula: C10 H10 O2
Ligand molecular weight: 162.185
Ligand SMILES: CC(=O)C=Cc1ccc(cc1)O
Ligand InChI: InChI=1S/C10H10O2/c1-8(11)2-3-9-4-6-10(12)7-5-9/h2-7,12H,1H3/b3-2+
Release date: 2018-02-28
The co-crystal structure of low molecular weight protein tyrosine phosphatase (LMW-PTP) with a small molecule inhibitor SPAA-2 (PDB entry 7UW6)
Macromolecule: Low molecular weight phosphotyrosine protein phosphatase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 177 residues
Sequence: MGSSHHHHHHSSGLVPRGSHAEQATKSVLFVCLGNICRSPIAEAVFRKLVTDQNISENWRVDSAATSGYEIGNPPDYRGQSCMKRHGIPMSHVARQITKEDFATFDYILCMDESNLRDLNRKSNQVKTCKAKIELLGSYDPQKQLIIEDPYYGNDSDFETVYQQCVRCCRAFLEKAH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.5
R work: 0.1611
R free: 0.1945
Average B factor: 28.6135
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: The crystallization buffer grid is 25-30% PEGME 5000 in 100 mM Bis-Tris, pH 6.0-6.5.

The final concentration of the ligand in the crystallization solution is 1 mM.
Matthews coefficient: 2.53
Solvent content (%): 51.31
Ligand: 2-[(1,3-benzothiazol-2-yl)amino]-2-oxoethane-1-sulfonic acid (OIF)
Ligand formula: C9 H8 N2 O4 S2
Ligand molecular weight: 272.301
Ligand SMILES: c1ccc2c(c1)nc(s2)NC(=O)CS(=O)(=O)O
Ligand InChI: InChI=1S/C9H8N2O4S2/c12-8(5-17(13,14)15)11-9-10-6-3-1-2-4-7(6)16-9/h1-4H,5H2,(H,10,11,12)(H,13,14,15)
Release date: 2022-10-19
USP34 catalytic domain (PDB entry 7W3R)
Macromolecule: Ubiquitin carboxyl-terminal hydrolase 34
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.19.12
Sequence length: 384 residues
Sequence: AECRFVGLTNLGATCYLASTIQQLYMIPEARQAVFTAKYSEDMKHKTTLLELQKMFTYLMESECKAYNPRPFCKTYTMDKQPLNTGEQKDMTEFFTDLITKIEEMSPELKNTVKSLFGGVITNNVVSLDCEHVSQTAEEFYTVRCQVADMKNIYESLDEVTIKDTLEGDNMYTCSHCGKKVRAEKRACFKKLPRILSFNTMRYTFNMVTMMKEKVNTHFSFPLRLDMTPYTEDFLMGKSERKEGFKEVSDHSKDSESYEYDLIGVTVHTGTADGGHYYSFIRDIVNPHAYKNNKWYLFNDAEVKPFDSAQLASECFGGEMTTKTYDSVTDKFMDFSFEKTHSAYMLFYKRMEPEEENGREYKFDVSSELLEWIWHDNMQFLQDK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.92
R work: 0.2259
R free: 0.2615
Average B factor: 50.2922
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 289
Crystal growth procedure: 16% w/v PEG 3350, 0.16M sodium bromide, 0.125M Magnesium formate dihydrate, 0.025M BIS-TRIS
Matthews coefficient: 2.3
Solvent content (%): 46.46
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: 2022-06-01
DNA Polymerase Lambda, dCTP:At Mn2+ Product State Ternary Complex, 960 min (PDB entry 7M4J)
Macromolecule: DNA polymerase lambda
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 329 residues
Sequence: AQPSSQKATNHNLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEKIIEILESGHLRKLDHISESVPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQASLTTQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDVLITHPDGRSHRGIFSRLLDSLRQEGFLTDDLVKGETKYLGVCRLPGPGRRHRRLDIIVVPYSEFACALLYFTGSAHFNRSMRALAKTKGMSLSEHALSTAVVRNTHGAKVGPGRVLPTPTEKDVFRLLGLPYREPAERDW
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.377
R work: 0.2256
R free: 0.2612
Average B factor: 53.3011
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 80-95mM BICINE pH 8.3, 0.3M Na-K Tartrate, 18-22.5% PolyPure PEG
Matthews coefficient: 2.87
Solvent content (%): 57.19
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: 2022-07-06
Crystal structure of human polymerase eta complexed with Xanthine containing DNA (PDB entry 6WK6)
Macromolecule: DNA polymerase eta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 432 residues
Sequence: MATGQDRVVALVDMDCFFVQVEQRQNPHLRNKPCAVVQYKSWKGGGIIAVSYEARAFGVTRSMWADDAKKLCPDLLLAQVRESRGKANLTKYREASVEVMEIMSRFAVIERASIDEAYVDLTSAVQERLQKLQGQPISADLLPSTYIEGLPQGPTTAEETVQKEGMRKQGLFQWLDSLQIDNLTSPDLQLTVGAVIVEEMRAAIERETGFQCSAGISHNKVLAKLACGLNKPNRQTLVSHGSVPQLFSQMPIRKIRSLGGKLGASVIEILGIEYMGELTQFTESQLQSHFGEKNGSWLYAMCRGIEHDPVKPRQLPKTIGCSKNFPGKTALATREQVQWWLLQLAQELEERLTKDRNDNDRVATQLVVSIRVQGDKRLSSLRRCCALTRYDAHKMSHDAFTVIKNCNTSGIQTEWSPPLTMLFLCATKFSAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.35
R work: 0.1886
R free: 0.2377
Average B factor: 48.18
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 100 mM MES pH 6
5 mM magnesium chloride
18% PEG 2000 MME
Matthews coefficient: 2.12
Solvent content (%): 41.9
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: 2021-01-06
Binary complex of human polymerase nu and DNA with the finger domain closed (PDB entry 4XVK)
Macromolecule: DNA polymerase nu
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 666 residues
Sequence: KKHFCDIRHLDDWAKSQLIEMLKQAAALVITVMYTDGSTQLGADQTPVSSVRGIVVLVKRQAEGGHGCPDAPACGPVLEGFVSDDPCIYIQIEHSAIWDQEQEAHQQFARNVLFQTMKCKCPVICFNAKDFVRIVLQFFGNDGSWKHVADFIGLDPRIAAWLIDPSDATPSFEDLVEKYCEKSITVKVNSTYGNSSRNIVNQNVRENLKTLYRLTMDLCSKLKDYGLWQLFRTLELPLIPILAVMESHAIQVNKEEMEKTSALLGARLKELEQEAHFVAGERFLITSNNQLREILFGKLKLHLLSQRNSLPRTGLQKYPSTSEAVLNALRDLHPLPKIILEYRQVHKIKSTFVDGLLACMKKGSISSTWNQTGTVTGRLSAKHPNIQGISKHPIQITTPKNFKGKEDKILTISPRAMFVSSKGHTFLAADFSQIELRILTHLSGDPELLKLFQESERDDVFSTLTSQWKDVPVEQVTHADREQTKKVVYAVVYGAGKERLAACLGVPIQEAAQFLESFLQKYKKIKDFARAAIAQCHQTGCVVSIMGRRRPLPRIHAHDQQLRAQAERQAVNFVVQGSAADLCKLAMIHVFTAVAASHTLTARLVAQIHDELLFEVEDPQIPECAALVRRTMESLEQVQALELQLQVPLKVSLSAGRSWGHLVPLQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.95
R work: 0.2221
R free: 0.2411
Average B factor: 75.1607
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 293
Crystal growth procedure: 1.5 M Ammonium Sulfate, 100 mM MES
Matthews coefficient: 5.66
Solvent content (%): 78.11
Ligand: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID (MES)
Ligand formula: C6 H13 N O4 S
Ligand molecular weight: 195.237
Ligand SMILES: C1COCC[NH+]1CCS(=O)(=O)[O-]
Ligand InChI: InChI=1S/C6H13NO4S/c8-12(9,10)6-3-7-1-4-11-5-2-7/h1-6H2,(H,8,9,10)
Release date: 2015-03-11
GDP-bound KRAS G12D in complex with TH-Z816 (PDB entry 7EW9)
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: GMTEYKLVVVGADGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.13
R work: 0.2009
R free: 0.2568
Average B factor: 39.1453
Crystallization method: EVAPORATION
Crystallization pH: 8.5
Crystallization temperature (K): 293.15
Crystal growth procedure: 0.2 M sodium acetate, 0.1 M Tris, pH 8.5, 26 % (w/v) PEG 3350
Matthews coefficient: 2.26
Solvent content (%): 45.47
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: 2021-12-29
Structure of CHK1 10-pt. mutant complex with aminopyridine LRRK2 inhibitor (PDB entry 5OPR)
Macromolecule: Serine/threonine-protein kinase Chk1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 297 residues
Sequence: MAVPFVEDWDLVQTLGEGAYGEVQLAVNRVTEEAVAVKIVDMKRAVDCPENIKKEICILKMLNHENVIKFYGHRREGNIQYLFMELASGGSLFDRIEPDIGMPEPDAQRFFHQLMAGVVYLHGIGITHRDIKPHNLLLDERDNLKIADYSLATVFRYNNRERLLNKMCGTLPYVAPELLKRREFHAEPVDVWSCGIVLTAMLAGELPWDQPSDSCQEYSDWKEKKTYLNPWKKIDSAPLALLHKILVENPSARITIPDIKKDRWYNKPLKKGAKRPRVTSGGVSESPSGHHHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.95
R work: 0.1636
R free: 0.2061
Average B factor: 41.893
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 7% PEG 8000, 0.1 M MES buffer pH 6.5, 20% ethylene glycol
Matthews coefficient: 2.31
Solvent content (%): 46.65
Ligand: 5-[4-(morpholin-4-ylmethyl)phenyl]-3-(1-propan-2-yl-1,2,3-triazol-4-yl)pyridin-2-amine (A3E)
Ligand formula: C21 H26 N6 O
Ligand molecular weight: 378.471
Ligand SMILES: CC(C)n1cc(nn1)c2cc(cnc2N)c3ccc(cc3)CN4CCOCC4
Ligand InChI: InChI=1S/C21H26N6O/c1-15(2)27-14-20(24-25-27)19-11-18(12-23-21(19)22)17-5-3-16(4-6-17)13-26-7-9-28-10-8-26/h3-6,11-12,14-15H,7-10,13H2,1-2H3,(H2,22,23)
Release date: 2017-10-25
CA IX mimic Complexed with Steroidal Sulfamate Compound STX 2845 (PDB entry 6E92)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 257 residues
Sequence: HWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHSFQVTFDDSQDKAVLKGGPLDGTYRLLQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDVGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTEGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLAECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.772
R work: 0.1514
R free: 0.1891
Average B factor: 23.2475
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 298
Crystal growth procedure: 1.6M NaCitrate
50mM Tris
Matthews coefficient: 2.17
Solvent content (%): 43.19
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: 2019-03-27
Crystal structure of Q38A human DNA polymerase eta bound with 8-oxoadenine (oxoA) and non-hydrolyzable dGTP analog (dGTP*) (PDB entry 6UQI)
Macromolecule: DNA polymerase eta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 435 residues
Sequence: GPHMATGQDRVVALVDMDCFFVQVEQRQNPHLRNKPCAVVAYKSWKGGGIIAVSYEARAFGVTRSMWADDAKKLCPDLLLAQVRESRGKANLTKYREASVEVMEIMSRFAVIERASIDEAYVDLTSAVQERLQKLQGQPISADLLPSTYIEGLPQGPTTAEETVQKEGMRKQGLFQWLDSLQIDNLTSPDLQLTVGAVIVEEMRAAIERETGFQCSAGISHNKVLAKLACGLNKPNRQTLVSHGSVPQLFSQMPIRKIRSLGGKLGASVIEILGIEYMGELTQFTESQLQSHFGEKNGSWLYAMCRGIEHDPVKPRQLPKTIGCSKNFPGKTALATREQVQWWLLQLAQELEERLTKDRNDNDRVATQLVVSIRVQGDKRLSSLRRCCALTRYDAHKMSHDAFTVIKNCNTSGIQTEWSPPLTMLFLCATKFSAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.179
R free: 0.239
Average B factor: 43.75
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M MES, 5 mM MgCl2, 12-21% (w/v) PEG 2K-MME, pH 6.0
Matthews coefficient: 2.1
Solvent content (%): 41.53
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: 2020-10-28
ENTEROPEPTIDASE IN COMPLEX WITH COMPOUND 6 (PDB entry 6ZOV)
Macromolecule: Enteropeptidase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.9
Sequence length: 235 residues
Sequence: IVGGSDAKEGAWPWVVGLYYDDRLLCGASLVSSDWLVSAAHCVYGRNLEPSKWTAILGLHMKSNLTSPQTVPRLIDEIVINPHYNRRRKDNDIAMMHLEFKVNYTDYIQPISLPEENQVFPPGRNCSIAGWGTVVYQGTTADILQEADVPLLSNERCQQQMPEYNITENMICAGYEEGGIDSCQGDSGGPLMCQENNRWFLAGVTSFGYECALPNRPGVYARVSRFTEWIQSFLH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.19
R work: 0.2262
R free: 0.2504
Average B factor: 34.429
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.25
Crystallization temperature (K): 293
Crystal growth procedure: PEG20000
Matthews coefficient: 2.73
Solvent content (%): 55.05
Ligand: 4-carbamimidamidobenzoic acid (GBS)
Ligand formula: C8 H9 N3 O2
Ligand molecular weight: 179.176
Ligand SMILES: c1cc(ccc1C(=O)O)NC(=N)N
Ligand InChI: InChI=1S/C8H9N3O2/c9-8(10)11-6-3-1-5(2-4-6)7(12)13/h1-4H,(H,12,13)(H4,9,10,11)
Release date: 2020-10-21