satarupa22/MacromolecularLigandDB huggingface dataset:
Non-receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitor SHP836 (PDB entry 5EHP)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 11
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 526 residues
Sequence: SMTSRRWFHPNITGVEAENLLLTRGVDGSFLARPSKSNPGDFTLSVRRNGAVTHIKIQNTGDYYDLYGGEKFATLAELVQYYMEHHGQLKEKNGDVIELKYPLNCADPTSERWFHGHLSGKEAEKLLTEKGKHGSFLVRESQSHPGDFVLSVRTGDDKGESNDGKSKVTHVMIRCQELKYDVGGGERFDSLTDLVEHYKKNPMVETLGTVLQLKQPLNTTRINAAEIESRVRELSKLAETTDKVKQGFWEEFETLQQQECKLLYSRKEGQRQENKNKNRYKNILPFDHTRVVLHDGDPNEPVSDYINANIIMPEFETKCNNSKPKKSYIATQGCLQNTVNDFWRMVFQENSRVIVMTTKEVERGKSKCVKYWPDEYALKEYGVMRVRNVKESAAHDYTLRELKLSKVGQGNTERTVWQYHFRTWPDHGVPSDPGGVLDFLEEVHHKQESIMDAGPVVVHCSAGIGRTGTFIVIDILIDIIREKGVDCDIDVPKTIQMVRSQRSGMVQTEAQYRFIYMAVQHYIETL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.85
R work: 0.1745
R free: 0.2084
Average B factor: 34.24
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 17% PEG 3350, 200mM Ammonium Phosphate
Matthews coefficient: 2.28
Solvent content (%): 46.04
Ligand: 5-[2,3-bis(chloranyl)phenyl]-2-[(3~{R},5~{S})-3,5-dimethylpiperazin-1-yl]pyrimidin-4-amine (5OA)
Ligand formula: C16 H19 Cl2 N5
Ligand molecular weight: 352.262
Ligand SMILES: CC1CN(CC(N1)C)c2ncc(c(n2)N)c3cccc(c3Cl)Cl
Ligand InChI: InChI=1S/C16H19Cl2N5/c1-9-7-23(8-10(2)21-9)16-20-6-12(15(19)22-16)11-4-3-5-13(17)14(11)18/h3-6,9-10,21H,7-8H2,1-2H3,(H2,19,20,22)/t9-,10+
Release date: 2016-07-06
Crystal Structure of the Cancer Genomic DNA Mutator APOBEC3B with loop 7 from APOBEC3G (PDB entry 6NFM)
Macromolecule: DNA dC->dU-editing enzyme APOBEC-3B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.4.38
Sequence length: 193 residues
Sequence: MEILRYLMDPDTFTSNFNNDPLVLRRRQTYLCYEVERLDNGTSVKMDQHMGFLCNESGRHAELRFLDLVPSLQLDPAQIYRVTWFISWSPCFSWGCAGEVRAFLQENTHVRLRIKAARIYDDQGRCQEALQMLRDAGAQVSIMTYDEFEYCWDTFVYRQGCPFQPWDGLEEHSQALSGRLRAILQLEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.53
R work: 0.2181
R free: 0.2757
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: LiCl, HEPES,PEG3350
Matthews coefficient: 2.08
Solvent content (%): 40.73
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: 2019-12-25
Structure of Hs/AcPRC2 in complex with a pyridone inhibitor (PDB entry 5IJ7)
Macromolecule: Enhancer of Zeste Homolog 2 (EZH2),Histone-lysine N-methyltransferase EZH2
Type: Protein, polypeptide(L)
Source organism: Anolis carolinensis
EC number: 2.1.1.43
Sequence length: 643 residues
Sequence: MGQTGKKSEKGPICWRKRVKSEYMRLRQLKRFRRADEVKSMFNSNRQKIQERTEILNQEWKQRRIQPVHIMTSVSSLRGTRECSVTSDLDFPKQVIPLKTLNAVASVPIMYSWSPLQQNFMVEDETVLHNIPYMGDEVLDQDGTFIEELIKNYDGKVHGDRECGFINDEIFVELVNALGQLDRRDEKQKNQESNQIDKESHPPRKFPSDKIFEAISSMFPDKGTAEELKEKYKELTEQQLPGALPPECTPNIDGPNAKSVQREQSLHSFHTLFCRRCFKYDCFLHPFHATPNTYKRKNTEMAIDNKPCGPHCYQHLEGAKEFAAALTAENVEWSGAEASMFRVLIGTYYDNFCAIARLIGTKTCRQVYEFRVKESSIIAPAPAEDVDTLGGGGSGGGGSGGGGSAAADGSSNHVYNYQPCDHPRQPCDNSCPCVIAQNFCEKFCQCSSECQNRFPGCRCKAQCNTKQCPCYLAVRECDPDLCLTCGAADHWDSKNVSCKNCSIQRGSKKHLLLAPSDVAGWGIFIKDPVQKNEFISEYCGEIISQDEADRRGKVYDKYMCSFLFNLNNDFVVDATRKGNKIRFANHSVNPNCYAKVMMVNGDHRIGIFAKRAIQTGEELFFDYRYSQADALKYVGIEREMEIP
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.62
R work: 0.1912
R free: 0.238
Average B factor: 68.45
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.6
Crystallization temperature (K): 286
Crystal growth procedure: 24.0 %w/v PEG monomethyl ether 2000,
0.0050 M TCEP hydrochloride, 0.1 M Bis_tris (pH 6.60)
Matthews coefficient: 2.18
Solvent content (%): 43.63
Ligand: 5,8-dichloro-2-[(4-ethyl-6-methyl-2-oxo-1,2-dihydropyridin-3-yl)methyl]-7-({1-[(2R)-2-hydroxypropanoyl]piperidin-4-yl}oxy)-3,4-dihydroisoquinolin-1(2H)-one (6BN)
Ligand formula: C26 H31 Cl2 N3 O5
Ligand molecular weight: 536.447
Ligand SMILES: CCC1=C(C(=O)NC(=C1)C)CN2CCc3c(cc(c(c3C2=O)Cl)OC4CCN(CC4)C(=O)C(C)O)Cl
Ligand InChI: InChI=1S/C26H31Cl2N3O5/c1-4-16-11-14(2)29-24(33)19(16)13-31-10-7-18-20(27)12-21(23(28)22(18)26(31)35)36-17-5-8-30(9-6-17)25(34)15(3)32/h11-12,15,17,32H,4-10,13H2,1-3H3,(H,29,33)/t15-/m1/s1
Release date: 2016-05-04
Human PRPF4B bound to benzothiophene inhibitor 224 (PDB entry 6PJJ)
Macromolecule: Serine/threonine-protein kinase PRP4 homolog
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 351 residues
Sequence: SMDFKENPNLRDNWTDAEGYYRVNIGEVLDKRYNVYGYTGQGVFSNVVRARDNARANQEVAVKIIRNNELMQKTGLKELEFLKKLNDADPDDKFHCLRLLRHFYHKQHLCLVFEPLSMNLREVLKKYGKDVGLHIKAVRSYSQQLFLALKLLKRCNILHADIKPDNILVNESKTILKLCDFGSASHVADNDITPYLFSRFYRAPEIIIGKSYDYGIDMWSVGCTLYELYTGKILFPGKTNNHMLKLAMDLKGKMPNKMIRKGVFKDQHFDQNLNFMYIEVDKVTEREKVTVMSTINPTKDLLADLIGCQRLPEDQRKKVHQLKDLLDQILMLDPAKRISINQALQHAFIQE
Oligomeric state: Homo 4-mer
Stoichiometry: A4
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.4
R work: 0.1903
R free: 0.2402
Average B factor: 32.956
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M HEPES pH 7.5, 0.1M Na/K phosphate, 15% PEG smear high, 10% etylene glycol
Matthews coefficient: 2.59
Solvent content (%): 52.46
Ligand: 4-(5-{[(3-aminophenyl)methyl]carbamoyl}thiophen-2-yl)-1-benzothiophene-2-carboxamide (OCJ)
Ligand formula: C21 H17 N3 O2 S2
Ligand molecular weight: 407.509
Ligand SMILES: c1cc(cc(c1)N)CNC(=O)c2ccc(s2)c3cccc4c3cc(s4)C(=O)N
Ligand InChI: InChI=1S/C21H17N3O2S2/c22-13-4-1-3-12(9-13)11-24-21(26)18-8-7-17(27-18)14-5-2-6-16-15(14)10-19(28-16)20(23)25/h1-10H,11,22H2,(H2,23,25)(H,24,26)
Release date: 2019-08-28
Structure of Human NMT2 with myristoyl-lysine peptide and CoA products (PDB entry 6PAU)
Macromolecule: Glycylpeptide N-tetradecanoyltransferase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.97
Sequence length: 383 residues
Sequence: KHRYQFWDTQPVPKLDEVITSHGAIEPDKDNVRQEPYSLPQGFMWDTLDLSDAEVLKELYTLLNENYVEDDDNMFRFDYSPEFLLWALRPPGWLLQWHCGVRVSSNKKLVGFISAIPANIRIYDSVKKMVEINFLCVHKKLRSKRVAPVLIREITRRVNLEGIFQAVYTAGVVLPKPIATCRYWHRSLNPRKLVEVKFSHLSRNMTLQRTMKLYRLPDVTKTSGLRPMEPKDIKSVRELINTYLKQFHLAPVMDEEEVAHWFLPREHIIDTFVVESPNGKLTDFLSFYTLPSTVMHHPAHKSLKAAYSFYNIHTETPLLDLMSDALILAKSKGFDVFNALDLMENKTFLEKLKFGIGDGNLQYYLYNWRCPGTDSEKVGLVLQ
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.93
R work: 0.1973
R free: 0.2177
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 8 mg/mL protein in a buffer of 25 mM Tris-HCl pH 7.5, 120 mM NaCl, 1 mM DTT, 1 mM MgCl2, mixed 1:1 with well solution of 22% PEG 8000, 0.1 M Bis-Tris pH 6.5
Matthews coefficient: 2.18
Solvent content (%): 43.64
Ligand: GLYCEROL (GOL)
Ligand formula: C3 H8 O3
Ligand molecular weight: 92.094
Ligand SMILES: C(C(CO)O)O
Ligand InChI: InChI=1S/C3H8O3/c4-1-3(6)2-5/h3-6H,1-2H2
Release date: 2020-03-11
Carbonic anhydrase II in complex with Hit3-t2 (MH174) (PDB entry 7OYQ)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 260 residues
Sequence: MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.15
R work: 0.1432
R free: 0.1805
Average B factor: 16.202
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 291
Crystal growth procedure: 1.6 M sodium citrate, 50 mM Tris-H2SO4
Matthews coefficient: 2.09
Solvent content (%): 41.13
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: 2023-01-18
Crystal structure of SAM-bound PRDM9 in complex with MRK-740 inhibitor (PDB entry 6NM4)
Macromolecule: Histone-lysine N-methyltransferase PRDM9
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.43
Sequence length: 191 residues
Sequence: SEPQDDDYLYCEMCQNFFIDSCAAHGPPTFVKDSAVDKGHPNRSALSLPPGLRIGPSGIPQAGLGVWNEASDLPLGLHFGPYEGRITEDEEAANNGYSWLITKGRNCYEYVDGKDKSWANWMRYVNCARDDEEQNLVAFQYHRQIFYRTCRVIRPGCELLVWYGDEYGQELGIKWGSKWKKELMAGREPKP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.58
R work: 0.2072
R free: 0.2581
Average B factor: 61.466
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 0.1 M Bis-Tris, pH 6.0, 0.2 M ammonium acetate, 24.5% PEG3350
Matthews coefficient: 2.38
Solvent content (%): 48.3
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: 2019-02-13
Cytochrome 2C9 P450 inhibitor complex (PDB entry 5A5J)
Macromolecule: CYTOCHROME P450 2C9
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.99.38
Sequence length: 477 residues
Sequence: MAKKTSSGRGKLPPGPTPLPVIGNILQIGIKDISKSLTNLSKVYGPVFTLYFGLKPIVVLHGYEAVKEALIDLGEEFSGRGIFPLAERANRGFGIVFSNGKKWKEIRRFSLMTLRNFGMGKRSIEDRVQEEARCLVEELRKTKASPCDPTFILGCAPCNVICSIIFHKRFDYKDQQFLNLMEKLNENIKILSSPWIQICNNFSPIIDYFPGTHNKLLKNVAFMKSYILEKVKEHQESMDMNNPQDFIDCFLMKMEKEKHNQPSEFTIESLENTAVDLFGAGTETTSTTLRYALLLLLKHPEVTAKVQEEIERVIGRNRSPCMQDRSHMPYTDAVVHEVQRYIDLLPTSLPHAVTCDIKFRNYLIPKGTTILISLTSVLHDNKEFPNPEMFDPHHFLDEGGNFKKSKYFMPFSAGKRICVGEALAGMELFLFLTSILQNFNLKSLVDPKNLDTTPVVNGFASVPPFYQLCFIPIHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.9
R work: 0.21303
R free: 0.28792
Average B factor: 59.203
Matthews coefficient: 2.57
Solvent content (%): 52.08
Ligand: PROTOPORPHYRIN IX CONTAINING FE (HEM)
Ligand formula: C34 H32 Fe N4 O4
Ligand molecular weight: 616.487
Ligand SMILES: Cc1c2n3c(c1CCC(=O)O)C=C4C(=C(C5=[N]4[Fe]36[N]7=C(C=C8N6C(=C5)C(=C8C)C=C)C(=C(C7=C2)C)C=C)C)CCC(=O)O
Ligand InChI: InChI=1S/C34H34N4O4.Fe/c1-7-21-17(3)25-13-26-19(5)23(9-11-33(39)40)31(37-26)16-32-24(10-12-34(41)42)20(6)28(38-32)15-30-22(8-2)18(4)27(36-30)14-29(21)35-25;/h7-8,13-16H,1-2,9-12H2,3-6H3,(H4,35,36,37,38,39,40,41,42);/q;+2/p-2/b25-13-,26-13-,27-14-,28-15-,29-14-,30-15-,31-16-,32-16-;
Release date: 2016-08-03
Crystal structure of the F-BAR domain of PSTIPIP1 bound to the CTH domain of the phosphatase LYP (PDB entry 7AAM)
Macromolecule: Proline-serine-threonine phosphatase-interacting protein 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 292 residues
Sequence: GSHMMPQLQFKDAFWCRDFTAHTGYEVLLQRLLDGRKMCKDMEELLRQRAQAEERYGKELVQIARKAGGQTEINSLRASFDSLKQQMENVGSSHIQLALTLREELRSLEEFRERQKEQRKKYEAVMDRVQKSKLSLYKKAMESKKTYEQKCRDADDAEQAFERISANGHQKQVEKSQNKARQCKDSATEAERVYRQSIAQLEKVRAEWEQEHRTTCEAFQLQEFDRLTILRNALWVHSNQLSMQCVKDDELYEEVRLTLEGCSIDADIDSFIQAKSTGTEPPAPVPYQNYYD
Oligomeric state: Hetero 3-mer
Stoichiometry: A2, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.15
R work: 0.2049
R free: 0.2409
Average B factor: 33.12
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 298
Crystal growth procedure: 100 mM Bis-Tris-propane (pH=6.0), 20% (w/v) PEG 3350, 200 mM sodium citrate.
LYP-CTH peptide was soaked into preformed crystals of the F-BAR domain of PSTPIP1.
Matthews coefficient: 2.5
Solvent content (%): 53
Ligand: GLYCEROL (GOL)
Ligand formula: C3 H8 O3
Ligand molecular weight: 92.094
Ligand SMILES: C(C(CO)O)O
Ligand InChI: InChI=1S/C3H8O3/c4-1-3(6)2-5/h3-6H,1-2H2
Release date: 2022-02-23
Human Argonaute2 Bound to t1-U Target RNA (PDB entry 4Z4E)
Macromolecule: Protein argonaute-2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.26
Sequence length: 859 residues
Sequence: MYSGAGPALAPPAPPPPIQGYAFKPPPRPDFGTSGRTIKLQANFFEMDIPKIDIYHYELDIKPEKCPRRVNREIVEHMVQHFKTQIFGDRKPVFDGRKNLYTAMPLPIGRDKVELEVTLPGEGKDRIFKVSIKWVSCVSLQALHDALSGRLPSVPFETIQALDVVMRHLPSMRYTPVGRSFFTASEGCSNPLGGGREVWFGFHQSVRPSLWKMMLNIDVSATAFYKAQPVIEFVCEVLDFKSIEEQQKPLTDSQRVKFTKEIKGLKVEITHCGQMKRKYRVCNVTRRPASHQTFPLQQESGQTVECTVAQYFKDRHKLVLRYPHLPCLQVGQEQKHTYLPLEVCNIVAGQRCIKKLTDNQTSTMIRATARSAPDRQEEISKLMRSADFNTDPYVREFGIMVKDEMTDVTGRVLQPPSILYGGRNKAIATPVQGVWDMRNKQFHTGIEIKVWAIACFAPQRQCTEVHLKSFTEQLRKISRDAGMPIQGQPCFCKYAQGADSVEPMFRHLKNTYAGLQLVVVILPGKTPVYAEVKRVGDTVLGMATQCVQMKNVQRTTPQTLSNLCLKINVKLGGVNNILLPQGRPPVFQQPVIFLGADVTHPPAGDGKKPSIAAVVGSMDAHPNRYCATVRVQQHRQEIIQDLAAMVRELLIQFYKSTRFKPTRIIFYRDGVSEGQFQQVLHHELLAIREACIKLEKDYQPGITFIVVQKRHHTRLFCTDKNERVGKSGNIPAGTTVDTKITHPTEFDFYLCSHAGIQGTSRPSHYHVLWDDNRFSSDELQILTYQLCHTYVRCTRSVSIPAPAYYAHLVAFRARYHLVDKEHDSAEGSHTSGQSNGRDHQALAKAVQVHQDTLRTMYFA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.1575
R free: 0.1854
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: PEG 3350, Tris, Isopropanol, Phenol, Magnesium
Matthews coefficient: 2.11
Solvent content (%): 41.66
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: 2015-09-23
H. SAPIENS CK2 KINASE ALPHA SUBUNIT IN COMPLEX WITH THE ATP-COMPETITIVE INHIBITOR 5,6-DIBROMOBENZOTRIAZOLE AT PH 8.5 (PDB entry 7QGD)
Macromolecule: Casein kinase II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 399 residues
Sequence: MSGPVPSRARVYTDVNTHRPREYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVKDQARMGSSSMPGGSTPVSSANMMSGISSVPTPSPLGPLAGSPVIAAANPLGMPVPAAAGAQQLEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.1791
R free: 0.2206
Average B factor: 41.833
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 290
Crystal growth procedure: 20 mM sodium formate, 20 mM ammonium acetate, 20 mM sodium citrate tribasic dihydrate, 20 mM sodium potassium tartrate tetrahydrate, 20 mM sodium oxamate, 20% polyethylene glycol 550 monomethyl ester, 10% polyethylene glycol 20 000, and 0.1 M buffering solution of Tris/BICINE pH 8.5
Matthews coefficient: 2.76
Solvent content (%): 55.43
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: 2022-10-19
Human VKOR with warfarin (PDB entry 6WV3)
Macromolecule: Vitamin K epoxide reductase, termini restrained by green fluorescent protein
Type: Protein, polypeptide(L)
Source organism: Aequorea victoria
EC number: 1.17.4.4
Sequence length: 390 residues
Sequence: MSKGEELFTGVVPILVELDGDVNGHKFSVRGEGEGDATNGKLTLKFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKRHDFFKSAMPEGYVQERTISFKDDGTYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNSTWGSPGWVRLALCLTGLVLSLYALHVKAARARDRDYRALCDVGTAISCSRVFSSRWGRGFGLVEHVLGQDSILNQSNSIFGCIFYTLQLLLGCLRTRWASVLMLLSSLVSLAGSVYLAWILFFVLYDFCIVCITTYAINVSLMWLSFRKVQENSHNVYITADKQKNGIKANFKIRHNVEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSVLSKDPNEKRDHMVLLEFVTAAGITHHHHHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.197
R work: 0.2009
R free: 0.2227
Average B factor: 46.3503
Crystallization method: LIPIDIC CUBIC PHASE
Crystallization pH: 6.5
Crystallization temperature (K): 295
Crystal growth procedure: 37% PEG400, 0.1 M MES, pH 6.5
Matthews coefficient: 2.91
Solvent content (%): 57.69
Ligand: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate (OLC)
Ligand formula: C21 H40 O4
Ligand molecular weight: 356.54
Ligand SMILES: CCCCCCCCC=CCCCCCCCC(=O)OCC(CO)O
Ligand InChI: InChI=1S/C21H40O4/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-21(24)25-19-20(23)18-22/h9-10,20,22-23H,2-8,11-19H2,1H3/b10-9-/t20-/m1/s1
Release date: 2020-11-11
Crystal structure of factor IXa variant V16I K98T Y177T I213V in complex with PPACK (PDB entry 5JBC)
Macromolecule: Coagulation factor IX
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.22
Sequence length: 58 residues
Sequence: CNIKNGRCEQFCKNSADNKVVCSCTEGYRLAENQKSCEPAVPFPCGRVSVSQTSKLTR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.1659
R free: 0.213
Average B factor: 45.21
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 6 mg/mL protein-inhibitor complex, 
0.1M MES pH 6.5, 
20% PEG6000
Matthews coefficient: 2.18
Solvent content (%): 43.69
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: 2016-06-01
Crystal structure of human tyrosinase related protein 1 mutant (T391V-R374S-Y362F) in complex with phenylthiourea (PTU) (PDB entry 5M8S)
Macromolecule: 5,6-dihydroxyindole-2-carboxylic acid oxidase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.18
Sequence length: 446 residues
Sequence: QFPRQCATVEALRSGMCCPDLSPVSGPGTDRCGSSSGRGRCEAVTADSRPHSPQYPHDGRDDREVWPLRFFNRTCHCNGNFSGHNCGTCRPGWRGAACDQRVLIVRRNLLDLSKEEKNHFVRALDMAKRTTHPLFVIATRRSEEILGPDGNTPQFENISIYNYFVWTHYYSVKKTFLGVGQESFGEVDFSHEGPAFLTWHRYHLLRLEKDMQEMLQEPSFSLPYWNFATGKNVCDICTDDLMGSRSNFDSTLISPNSVFSQWRVVCDSLEDYDTLGTLCNSTEDGPIRRNPAGNVARPMVQRLPEPQDVAQCLEVGLFDTPPFYSNSTNSFRNTVEGFSDPTGKYDPAVSSLHNLAHLFLNGTGGQVHLSPNDPIFVLLHTFTDAVFDEWLRRYNADISTFPLENAPIGHNRQYNMVPFWPPVTNTEMFVTAPDNLGYTYEIQWPS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.1936
R free: 0.2349
Average B factor: 44.2635
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 290
Crystal growth procedure: 0.1 M Tris (pH 7.0),
0.2 M NaCl and 30% (w/v) PEG 3000
Matthews coefficient: 3.03
Solvent content (%): 59.39
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: 2018-01-31
Human DNA Ligase 1 (E346A/E592A) Bound to an Adenylated, dideoxy Terminated DNA nick with 200 mM Mg2+ (PDB entry 6P0B)
Macromolecule: DNA ligase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.5.1.1
Sequence length: 645 residues
Sequence: SNDPSGYNPAKNNYHPVEDACWKPGQKVPYLAVARTFEKIEEVSARLRMVETLSNLLRSVVALSPPDLLPVLYLSLNHLGPPQQGLALGVGDGVLLKAVAQATGRQLESVRAEAAEKGDVGLVAENSRSTQRLMLPPPPLTASGVFSKFRDIARLTGSASTAKKIDIIKGLFVACRHSEARFIARSLSGRLRLGLAEQSVLAALSQAVSLTPPGQEFPPAMVDAGKGKTAEARKTWLEEQGMILKQTFCEVPDLDRIIPVLLEHGLERLPEHCKLSPGIPLKPMLAHPTRGISEVLKRFEEAAFTCEYKYDGQRAQIHALEGGEVKIFSRNQADNTGKYPDIISRIPKIKLPSVTSFILDTEAVAWDREKKQIQPFQVLTTRKRKEVDASEIQVQVCLYAFDLIYLNGESLVREPLSRRRQLLRENFVETEGEFVFATSLDTKDIEQIAEFLEQSVKDSCEGLMVKTLDVDATYEIAKRSHNWLKLKKDYLDGVGDTLDLVVIGAYLGRGKRAGRYGGFLLASYDEDSEELQAICKLGTGFSDEELEEHHQSLKALVLPSPRPYVRIDGAVIPDHWLDPSAVWEVKCADLSLSPIYPAARGLVDSDKGISLRFPRFIRVREDKQPEQATTSAQVACLYRKQSQIQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.203
R work: 0.1699
R free: 0.2056
Average B factor: 54.7983
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 293
Crystal growth procedure: 100 mM MES, 100 mM Lithium Acetate, 15% (w/v) PEG 3350
Matthews coefficient: 2.55
Solvent content (%): 51.72
Ligand: DI(HYDROXYETHYL)ETHER (PEG)
Ligand formula: C4 H10 O3
Ligand molecular weight: 106.12
Ligand SMILES: C(COCCO)O
Ligand InChI: InChI=1S/C4H10O3/c5-1-3-7-4-2-6/h5-6H,1-4H2
Release date: 2019-12-11
Human CDK1/CyclinB1/CKS2 With Inhibitor (PDB entry 4Y72)
Macromolecule: Cyclin-dependent kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.22
Sequence length: 302 residues
Sequence: GPLGSMEDYTKIEKIGEGTYGVVYKGRHKTTGQVVAMKKIRLESEEEGVPSTAIREISLLKELRHPNIVSLQDVLMQDSRLYLIFEFLSMDLKKYLDSIPPGQYMDSSLVKSYLYQILQGIVFCHSRRVLHRDLKPQNLLIDDKGTIKLADFGLARAFGIPIRVYTHEVVTLWYRSPEVLLGSARYSTPVDIWSIGTIFAELATKKPLFHGDSEIDQLFRIFRALGTPNNEVWPEVESLQDYKNTFPKWKPGSLASHVKNLDENGLDLLSKMLIYDPAKRISGKMALNHPYFNDLDNQIKKM
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.1861
R free: 0.2519
Average B factor: 48.7092
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 6.7
Crystallization temperature (K): 277
Crystal growth procedure: Conditions around 0.1M MES/imidazole buffer (pH6.7), 6.5% MPD, 5% PEG4K, 10% PEG1K
Protein at 10-12 mg/ml
Matthews coefficient: 2.45
Solvent content (%): 49.74
Ligand: {[(2,6-difluorophenyl)carbonyl]amino}-N-(4-fluorophenyl)-1H-pyrazole-3-carboxamide (LZ9)
Ligand formula: C17 H11 F3 N4 O2
Ligand molecular weight: 360.29
Ligand SMILES: c1cc(c(c(c1)F)C(=O)Nc2c[nH]nc2C(=O)Nc3ccc(cc3)F)F
Ligand InChI: InChI=1S/C17H11F3N4O2/c18-9-4-6-10(7-5-9)22-17(26)15-13(8-21-24-15)23-16(25)14-11(19)2-1-3-12(14)20/h1-8H,(H,21,24)(H,22,26)(H,23,25)
Release date: 2015-08-12
Crystal structure of NHL domain of TRIM2 (full C-terminal) (PDB entry 7QRV)
Macromolecule: Tripartite motif-containing protein 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.27
Sequence length: 281 residues
Sequence: SMNPIEDDLIFRVGTKGRNKGEFTNLQGVAASTNGKILIADSNNQCVQIFSNDGQFKSRFGIRGRSPGQLQRPTGVAVHPSGDIIIADYDNKWVSIFSSDGKFKTKIGSGKLMGPKGVSVDRNGHIIVVDNKACCVFIFQPNGKIVTRFGSRGNGDRQFAGPHFAAVNSNNEIIITDFHNHSVKVFNQEGEFMLKFGSNGEGNGQFNAPTGVAVDSNGNIIVADWGNSRIQVFDGSGSFLSYINTSADPLYGPQGLALTSDGHVVVADSGNHCFKVYRYLQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.45
R work: 0.1518
R free: 0.1779
Average B factor: 16.27
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293.15
Crystal growth procedure: 30% w/v PEG 5000 MME, 0.2 M Ammonium sulfate, 0.1M MES, pH 6.5
Matthews coefficient: 2.1
Solvent content (%): 41.31
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: 2022-05-04