satarupa22/MacromolecularLigandDB huggingface dataset:
X-ray structure of human PPAR gamma ligand binding domain-fenofibric acid co-crystals obtained by co-crystallization (PDB entry 7WGP)
Macromolecule: Isoform 1 of Peroxisome proliferator-activated receptor gamma
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 279 residues
Sequence: GSHMQLNPESADLRALAKHLYDSYIKSFPLTKAKARAILTGKTTDKSPFVIYDMNSLMMGEDKIKFKHITPLQEQSKEVAIRIFQGCQFRSVEAVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQEIYKDLY
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.53
R work: 0.2089
R free: 0.2686
Average B factor: 65.1647
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M Tris (pH 8.0), 1.1 M trisodium citrate
Matthews coefficient: 2.98
Solvent content (%): 58.69
Ligand: 2-[4-(4-chlorobenzene-1-carbonyl)phenoxy]-2-methylpropanoic acid (F5A)
Ligand formula: C17 H15 Cl O4
Ligand molecular weight: 318.752
Ligand SMILES: CC(C)(C(=O)O)Oc1ccc(cc1)C(=O)c2ccc(cc2)Cl
Ligand InChI: InChI=1S/C17H15ClO4/c1-17(2,16(20)21)22-14-9-5-12(6-10-14)15(19)11-3-7-13(18)8-4-11/h3-10H,1-2H3,(H,20,21)
Release date: 2022-05-25
Crystal Structure of the SRAP Domain of Human HMCES Protein (PDB entry 5KO9)
Macromolecule: Embryonic stem cell-specific 5-hydroxymethylcytosine-binding protein
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4
Sequence length: 277 residues
Sequence: MCGRTSCHLPRDVLTRACAYQDRRGQQRLPEWRDPDKYCPSYNKSPQSNSPVLLSRLHFEKDADSSERIIAPMRWGLVPSWFKESDPSKLQFNTTNCRSDTVMEKRSFKVPLGKGRRCVVLADGFYEWQRCQGTNQRQPYFIYFPQIKTEKSGSIGAADSPENWEKVWDNWRLLTMAGIFDCWEPPEGGDVLYSYTIITVDSCKGLSDIHHRMPAILDGEEAVSKWLDFGEVSTQEALKLIHPTENITFHAVSSVVNNSRNNTPECLAPVAENLYFQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.5
R work: 0.1818
R free: 0.2093
Average B factor: 24.169
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M BTP, 2% Tacsimate, 20% PEG3350
Matthews coefficient: 2.44
Solvent content (%): 44.89
Ligand: UNKNOWN ATOM OR ION (UNX)
Ligand formula: X
Ligand SMILES: *
Release date: 2016-08-24
Inhibitor binding to HDAC2 (PDB entry 8A0B)
Macromolecule: Histone deacetylase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.1.98
Sequence length: 498 residues
Sequence: MAYSQGGGKKKVCYYYDGDIGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKATAEEMTKYHSDEYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVAGAVKLNRQQTDMAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNFPMRDGIDDESYGQIFKPIISKVMEMYQPSAVVLQCGADSLSGDRLGCFNLTVKGHAKCVEVVKTFNLPLLMLGGGGYTIRNVARCWTYETAVALDCEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTPEYMEKIKQRLFENLRMLPHAPGVQMQAIPEDAVHEDSGDEDGEDPDKRISIRASDKRIACDEEFSDSEDEGEGGRRNVADHKKGAKKARIEEDKKETEDKKTDVKEEDKSKDNSGEKTDTKGTKSEQLSNPGSSGHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.746
R work: 0.165
R free: 0.188
Average B factor: 32.91
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 41% PEG 300
.1M pH=8.8 CHES/NaOH
Solvent content (%): 33.75
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2022-09-21
Crystal structure of D1228V c-MET bound by compound 15 (PDB entry 8OUV)
Macromolecule: Hepatocyte growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 309 residues
Sequence: GDSDISSPLLQNTVHIDLSALNPELVQAVQHVVIGPSSLIVHFNEVIGRGHFGCVYHGTLLDNDGKKIHCAVKSLNRITDIGEVSQFLTEGIIMKDFSHPNVLSLLGICLRSEGSPLVVLPYMKHGDLRNFIRNETHNPTVKDLIGFGLQVAKGMKYLASKKFVHRDLAARNCMLDEKFTVKVADFGLARVMYDKEYYSVHNKTGAKLPVKWMALESLQTQKFTTKSDVWSFGVLLWELMTRGAPPYPDVNTFDITVYLLQGRRLLQPEYCPDPLYEVMLKCWHPKAEMRPSFSELVSRISAIFSTFIG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.783
R work: 0.1912
R free: 0.2197
Average B factor: 29.69
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 293
Crystal growth procedure: 30 % PEG400, 0.1 M CaCl2, 0.1 M PCPT pH 4.5.
Matthews coefficient: 2.34
Solvent content (%): 47.51
Ligand: 5-(1H-indazol-7-yl)-1-[(1S)-1-phenylethyl]pyrimidine-2,4-dione (W3R)
Ligand formula: C19 H16 N4 O2
Ligand molecular weight: 332.356
Ligand SMILES: CC(c1ccccc1)N2C=C(C(=O)NC2=O)c3cccc4c3[nH]nc4
Ligand InChI: InChI=1S/C19H16N4O2/c1-12(13-6-3-2-4-7-13)23-11-16(18(24)21-19(23)25)15-9-5-8-14-10-20-22-17(14)15/h2-12H,1H3,(H,20,22)(H,21,24,25)/t12-/m0/s1
Release date: 2023-07-05
Rapid Discovery of Pyrido[3,4-d]pyrimidine Inhibitors of Monopolar Spindle kinase 1 (MPS1) Using a Structure-Based Hydridization Approach (PDB entry 5EI2)
Macromolecule: Dual specificity protein kinase TTK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 313 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSMSVKGRIYSILKQIGSGGSSKVFQVLNEKKQIYAIKYVNLEEADNQTLDSYRNEIAYLNKLQQHSDKIIRLYDYEITDQYIYMVMECGNIDLNSWLKKKKSIDPWERKSYWKNMLEAVHTIHQHGIVHSDLKPANFLIVDGMLKLIDFGIANQMQPDTTSVVKDSQVGTVNYMPPEAIKDMSSSRENGKSKSKISPKSDVWSLGCILYYMTYGKTPFQQIINQISKLHAIIDPNHEIEFPDIPEKDLQDVLKCCLKRDPKQRISIPELLAHPYVQIQTHPVNQMAKGTTEE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.67
R work: 0.2358
R free: 0.295
Average B factor: 96.02
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 291.15
Crystal growth procedure: 0.1 M Bis-Tris propane
0.2 M MgCl2
0.2 M Sodium formate
20% PEG3350
Matthews coefficient: 2.73
Solvent content (%): 55
Ligand: ~{N}-(2,4-dimethoxyphenyl)-8-(1-methylpyrazol-4-yl)pyrido[3,4-d]pyrimidin-2-amine (5O7)
Ligand formula: C19 H18 N6 O2
Ligand molecular weight: 362.385
Ligand SMILES: Cn1cc(cn1)c2c3c(ccn2)cnc(n3)Nc4ccc(cc4OC)OC
Ligand InChI: InChI=1S/C19H18N6O2/c1-25-11-13(10-22-25)17-18-12(6-7-20-17)9-21-19(24-18)23-15-5-4-14(26-2)8-16(15)27-3/h4-11H,1-3H3,(H,21,23,24)
Release date: 2016-04-20
SYK catalytic domain complexed with a potent orally bioavailable thiazole inhibitor (PDB entry 5CXH)
Macromolecule: Tyrosine-protein kinase SYK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 289 residues
Sequence: MALEEIRPKEVYLDRKLLTLEDKELGSGNFGTVKKGYYQMKKVVKTVAVKILKNEANDPALKDELLAEANVMQQLDNPYIVRMIGICEAESWMLVMEMAELGPLNKYLQQNRHVTDKNIIELVHQVSMGMKYLEESNFVHRDLAARNVLLVTQHYAKISDFGLSKALRADENYYKAQTHGKWPVKWYAPECINYYKFSSKSDVWSFGVLMWEAFSYGQKPYRGMKGSEVTAMLEKGERMGCPAGCPREMYDLMNLCWTYDVENRPGFAAVELRLRNYYYDVVNHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.1746
R free: 0.2052
Average B factor: 25.85
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.3
Crystallization temperature (K): 277
Crystal growth procedure: 20% PEG3350, 0.2M potassium fluoride, no buffer pH 7.3
Matthews coefficient: 2.39
Solvent content (%): 48.49
Ligand: (4R)-4-[(1R)-1-{[6-(3,4-dimethoxyphenyl)[1,3]thiazolo[5,4-c]pyridin-4-yl]oxy}ethyl]pyrrolidin-2-one (55M)
Ligand formula: C20 H21 N3 O4 S
Ligand molecular weight: 399.463
Ligand SMILES: CC(C1CC(=O)NC1)Oc2c3c(cc(n2)c4ccc(c(c4)OC)OC)ncs3
Ligand InChI: InChI=1S/C20H21N3O4S/c1-11(13-7-18(24)21-9-13)27-20-19-15(22-10-28-19)8-14(23-20)12-4-5-16(25-2)17(6-12)26-3/h4-6,8,10-11,13H,7,9H2,1-3H3,(H,21,24)/t11-,13-/m1/s1
Release date: 2015-09-23
Crystal structure of human Pim-1 kinase in complex with a thiadiazolamine-indole inhibitor. (PDB entry 4WT6)
Macromolecule: Serine/threonine-protein kinase pim-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 286 residues
Sequence: MAHHHHHHDEVDGPLESQYQVGPLLGSGGFGSVYSGIRVSDNLPVAIKHVEKDRISDWGELPNGTRVPMEVVLLKKVSSGFSGVIRLLDWFERPDSFVLILERPEPVQDLFDFITERGALQEELARSFFWQVLEAVRHCHNCGVLHRDIKDENILIDLNRGELKLIDFGSGALLKDTVYTDFDGTRVYSPPEWIRYHRYHGRSAAVWSLGILLYDMVCGDIPFEHDEEIIRGQVFFRQRVSSECQHLIRWCLALRPSDRPTFEEIQNHPWMQDVLLPQETAEIHLH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.17625
R free: 0.21109
Average B factor: 43.464
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 277
Crystal growth procedure: 1.0M LiCl, 0.1M TRIS, 20% PEG6K
Matthews coefficient: 3.4
Solvent content (%): 63.83
Ligand: 6-[5-(5-amino-1,3,4-thiadiazol-2-yl)-1H-indol-3-yl]-N-cyclopentylpyridin-2-amine (3U6)
Ligand formula: C20 H20 N6 S
Ligand molecular weight: 376.478
Ligand SMILES: c1cc(nc(c1)NC2CCCC2)c3c[nH]c4c3cc(cc4)c5nnc(s5)N
Ligand InChI: InChI=1S/C20H20N6S/c21-20-26-25-19(27-20)12-8-9-16-14(10-12)15(11-22-16)17-6-3-7-18(24-17)23-13-4-1-2-5-13/h3,6-11,13,22H,1-2,4-5H2,(H2,21,26)(H,23,24)
Release date: 2015-02-11
JNK2/3 in complex with 3-(4-{[(4-methylphenyl)carbamoyl]amino}-1H-pyrazol-1-yl)-N-(2-methylpyridin-4-yl)benzamide (PDB entry 4W4Y)
Macromolecule: c-jun NH2-terminal kinase 3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.24
Sequence length: 366 residues
Sequence: MAMSKSKVDNQFYSVEVGDSTFTVLKRYQNLKPIGSGAQGIVCAAYDAVLDRNVAIKKLSRPFQNQTHAKRAYRELVLMKCVNHKNIISLLNVFTPQKTLEEFQDVYLVMELMDANLCQVIQMELDHERMSYLLYQMLCGIKHLHSAGIIHRDLKPSNIVVKSDCTLKILDFGLARTAGTSFMMTPYVVTRYYRAPEVILGMGYKENVDIWSVGCIMGEMVRHKILFPGRDYIDQWNKVIEQLGTPCPEFMKKLQPTVRNYVENRPKYAGLTFPKLFPDSLFPADSEHNKLKASQARDLLSKMLVIDPAKRISVDDALQHPYINVWYDPAEVEAPPPQIYDKQLDEREHTIEEWKELIYKEVMNSE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.1959
R free: 0.2598
Average B factor: 67.96
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: EG 3350, ammonium tartrate
Matthews coefficient: 2.43
Solvent content (%): 49.32
Ligand: 3-(4-{[(4-methylphenyl)carbamoyl]amino}-1H-pyrazol-1-yl)-N-(2-methylpyridin-4-yl)benzamide (3HQ)
Ligand formula: C24 H22 N6 O2
Ligand molecular weight: 426.47
Ligand SMILES: Cc1ccc(cc1)NC(=O)Nc2cnn(c2)c3cccc(c3)C(=O)Nc4ccnc(c4)C
Ligand InChI: InChI=1S/C24H22N6O2/c1-16-6-8-19(9-7-16)28-24(32)29-21-14-26-30(15-21)22-5-3-4-18(13-22)23(31)27-20-10-11-25-17(2)12-20/h3-15H,1-2H3,(H,25,27,31)(H2,28,29,32)
Release date: 2015-02-11
Human EXOG complexed with dRP-containing DNA (PDB entry 7R6T)
Macromolecule: Nuclease EXOG, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.30
Sequence length: 311 residues
Sequence: EKAVLEQFGFPLTGTEARCYTNHALSYDQAKRVPRWVLEHISKSKIMGDADRKHCKFKPDPNIPPTFSAFNEDYVGSGWSRGAMAPAGNNKFSSKAMAETFYLSNIVPQDFDNNSGYWNRIEMYCRELTERFEDVWVVSGPLTLPQTRGDGKKIVSYQVIGEDNVAVPSHLYKVILARRSSVSTEPLALGAFVVPNEAIGFQPQLTEFQVSLQDLEKLSGLVFFPHLDRTSDIRNICSVDTCKLLDFQEFTLYLSTRKIEGARSVLRLEKIMENLKNAEIEPDDYFMSRYEKKLEELKAKEQSGTQIRKPS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.9
R work: 0.229
R free: 0.286
Average B factor: 92.6
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 28% PEG 4K, 0.2 M Ammonium Acetate, 0.1 M Na Citrate tribasic dihydrate pH 5.6
Matthews coefficient: 2.38
Solvent content (%): 48.25
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: 2022-08-24
human carbonic anhydrase II in complex with ligand (PDB entry 5EH7)
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): 1.425
R work: 0.1454
R free: 0.1743
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 280
Crystal growth procedure: ammonium sulfate, tris chloride
Matthews coefficient: 2.1
Solvent content (%): 41.43
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: 2016-03-09
ERK2 mini-fragment binding (PDB entry 6QA3)
Macromolecule: Mitogen-activated protein kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.24
Sequence length: 368 residues
Sequence: MAHHHHHHMAAAAAAGAGPEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFEHQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKLLKTQHLSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLLNTTCDLKICDFGLARVADPDHDHTGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILGILGSPSQEDLNCIINLKARNYLLSLPHKNKVPWNRLFPNADSKALDLLDKMLTFNPHKRIEVEQALAHPYLEQYYDPSDEPIAEAPFKFDMELDDLPKEKLKELIFEETARFQPGYRS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.57
R work: 0.171
R free: 0.217
Average B factor: 27.287
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.2
Crystallization temperature (K): 293
Crystal growth procedure: 0.2M (NH4)2SO4
33% MPEG 2000
0.02M Mercaptoethanol
0.1M pH=7.2 HEPES/NaOH
Matthews coefficient: 2.26
Solvent content (%): 45.53
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: 2019-06-26
Crystal structure of human PCAF bromodomain in complex with fragment BR013 (fragment 3) (PDB entry 5FE2)
Macromolecule: Histone acetyltransferase KAT2B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 119 residues
Sequence: SMGKEKSKEPRDPDQLYSTLKSILQQVKSHQSAWPFMEPVKRTEAPGYYEVIRFPMDLKTMSERLKNRYYVSKKLFMADLQRVFTNCKEYNPPESEYYKCANILEKFFFSKIKEAGLID
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.25
R work: 0.2067
R free: 0.23651
Average B factor: 47.21
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277.15
Crystal growth procedure: 21-35% PEG 3350, 0.1 M Bis-Tris pH 5.5-7.0 or 21-40% medium-molecular-weight PEG smears (MMW PEG smears) buffered either with 0.1 M Bis-Tris pH 6.0-7.5 or 0.1 M Tris pH 7.5-8.8
Matthews coefficient: 3.37
Solvent content (%): 63.55
Ligand: 2-methyl-3~{H}-isoindol-1-one (5WV)
Ligand formula: C9 H9 N O
Ligand molecular weight: 147.174
Ligand SMILES: CN1Cc2ccccc2C1=O
Ligand InChI: InChI=1S/C9H9NO/c1-10-6-7-4-2-3-5-8(7)9(10)11/h2-5H,6H2,1H3
Release date: 2016-01-13
Human Carbonic Anhydrase II complexed with an inhibitor with a benzenesulfonamide group (4). (PDB entry 4YXU)
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): 1.08
R work: 0.1441
R free: 0.1633
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 291
Crystal growth procedure: 2.5 uL of the protein solution (10 mg/ml hCAII in 50 mM Tris pH 7.8) were mixed with 2.5 uL of the well solution (2.7 M (NH4)SO4, 100 mM Tris, pH 7.8, saturated with p-chloromercurybenzoicacid) and placed as a hanging drop. Crystals appeared after several days. The crystals were soaked in 3.0 M (NH4)SO4, 100 mM Tris, pH 7.8, saturated with the inhibitor, for 1 day.
Matthews coefficient: 2.08
Solvent content (%): 40.81
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: 2016-02-03
(4~{S},6~{S})-4-[2,4-bis(fluoranyl)phenyl]-6-(3,5-dimethyl-1,2-oxazol-4-yl)-4-methyl-5,6-dihydro-1,3-thiazin-2-amine (compound 5) bound to BACE1 (PDB entry 5KR8)
Macromolecule: Beta-secretase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.23.46
Sequence length: 455 residues
Sequence: MASMTGGQQMGRGSAGVLPAHGTQHGIRLPLRSGLGGAPLGLRLPRETDEEPEEPGRRGSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYNIPQTDEST
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.118
R work: 0.2127
R free: 0.244
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 6.4
Crystallization temperature (K): 295
Crystal growth procedure: 10% PEG5000 MME, 9% PEG8000, 0.2 M ammonium iodide, 0.2 M sodium citrate, pH 6.4
Matthews coefficient: 2.56
Solvent content (%): 51.9
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: 2016-09-07
Zn-Carbonic Anhydrase II complexed with 3NPA after UV at 200 K (PDB entry 7Y2I)
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): 1.4
R work: 0.11128
R free: 0.15874
Average B factor: 20.482
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 293
Crystal growth procedure: 1.3 M sodium citrate, 50 mM Tris-HCl
Matthews coefficient: 2.1
Solvent content (%): 41.43
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: 2023-12-20
Crystal Structure of TcdB2-TccC3-Cdc42 (PDB entry 6SUP)
Macromolecule: TcdB2,TccC3,Cell division control protein 42 homolog
Type: Protein, polypeptide(L)
Source organism: Photorhabdus luminescens
EC number: 3.6.5.2
Sequence length: 2128 residues
Sequence: GPDGMAALSLPLPISAGRGYAPAFTLNYNSGAGNSPFGLGWDCNVMTIRRRTHFGVPHYDETDTFLGPEGEVLVVADQPRDESTLQGINLGATFTVTGYRSRLESHFSRLEYWQPKTTGKTDFWLIYSPDGQVHLLGKSPQARISNPSQTTQTAQWLLEASVSSRGEQIYYQYRAEDDTGCEADEITHHLQATAQRYLHIVYYGNRTASETLPGLDGSAPSQADWLFYLVFDYGERSNNLKTPPAFSTTGSWLCRQDRFSRYEYGFEIRTRRLCRQVLMYHHLQALDSKITEHNGPTLVSRLILNYDESAIASTLVFVRRVGHEQDGNVVTLPPLELAYQDFSPRHHAHWQPMDVLANFNAIQRWQLVDLKGEGLPGLLYQDKGAWWYRSAQRLGEIGSDAVTWEKMQPLSVIPSLQSNASLVDINGDGQLDWVITGPGLRGYHSQRPDGSWTRFTPLNALPVEYTHPRAQLADLMGAGLSDLVLIGPKSVRLYANTRDGFAKGKDVVQSGDITLPVPGADPRKLVAFSDVLGSGQAHLVEVSATKVTCWPNLGRGRFGQPITLPGFSQPATEFNPAQVYLADLDGSGPTDLIYVHTNRLDIFLNKSGNGFAEPVTLRFPEGLRFDHTCQLQMADVQGLGVASLILSVPHMSPHHWRCDLTNMKPWLLNEMNNNMGVHHTLRYRSSSQFWLDEKAAALTTGQTPVCYLPFPIHTLWQTETEDEISGNKLVTTLRYARGAWDGREREFRGFGYVEQTDSHQLAQGNAPERTPPALTKNWYATGLPVIDNALSTEYWRDDQAFAGFSPRFTTWQDNKDVPLTPEDDNSRYWFNRALKGQLLRSELYGLDDSTNKHVPYTVTEFRSQVRRLQHTDSRYPVLWSSVVESRNYHYERIASDPQCSQNITLSSDRFGQPLKQLSVQYPRRQQPAINLYPDTLPDKLLANSYDDQQRQLRLTYQQSSWHHLTNNTVRVLGLPDSTRSDIFTYVAENVPAGGLNLELLSDKNSLIADDKPREYLGQQKTAYTDGQNTTPLQTPTRQALIAFTETTVFNQSTLSAFNGSIPSDKLSTTLEQAGYQQTNYLFPRTGEDKVWVAHHGYTDYGTAAQFWRPQKQSNTQLTGKITLIWDANYCVVVQTRDAAGLTTSAKYDWRFLTPVQLTDINDNQHLITLDALGRPITLRFWGTENGKMTGYSSPEKASFSPPSDVNAAIELKKPLPVAQCQVYAPESWMPVLSQKTFNRLAEQDWQKLYNARIITEDGRICTLAYRRWVQSQKAIPQLISLLNNGPRLPPHSLTLTTDRYDHDPEQQIRQQVVFSDGFGRLLQAAARHEAGMARQRNEDGSLIINVQHTENRWAVTGRTEYDNKGQPIRTYQPYFLNDWRYVSNDSARQEKEAYADTHVYDPIGREIKVITAKGWFRRTLFTPWFTVNEDENDTAAEVKKIDPKLYQKTPTVSVYDNRGLIIRNIDFHRTTANGDPDTRITRHQYDIHGHLNQSIDPRLYEAKQTNNTIKPNFLWQYDLTGNPLCTESIDAGRTVTLNDIEGRPLLTVTATGVIQTRQYETSSLPGRLLSVAEQTPEEKTSRITERLIWAGNTEAEKDHNLAGQCVRHYDTAGVTRLESLSLTGTVLSQSSQLLIDTQEANWTGDNETVWQNMLADDIYTTLSTFDATGALLTQTDAKGNIQRLAYDVAGQLNGSWLTLKGQTEQVIIKSLTYSAAGQKLREEHGNDVITEYSYEPETQRLIGIKTRRPSDTKVLQDLRYEYDPVGNVISIRNDAEATRFWHNQKVMPENTYTYDSLYQLISATGREMANIGQQSHQFPSPALPSDNNTYTNYTRTYTYDRGGNLTKIQHSSPATQNNYTTNITVSNRSNRAVLSTLTEDPAQVDALFDAGGHQNTLISGQNLNWNTRGELQQVTLVKRDKGANDDREWYRYSGDGRRMLKINEQQASNNAQTQRVTYLPNLELRLTQNSTATTEDLQVITVGEAGRAQVRVLHWESGKPEDIDNNQLRYSYDNLIGSSQLELDSEGQIISEEEYYPYGGTALWAARNQTEASYKTIRYSGKERDATGLYYYGYRYYQPWIGRWLSSDPAGTIDGLNLYRMVRNNPVTLLDPDGLNVFDEAILAALEP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.0
R work: 0.287
R free: 0.32
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 4.6
Crystallization temperature (K): 293.15
Crystal growth procedure: 0.1 M sodium chloride, 0.1 M magnesium chloride, 0.1 M tri-sodium citrate pH 5.5, 12 % PEG 4000
Seeding: 0.1 M magnesium chloride, 0.1 M tri-sodium acetate pH 4.6, 12 % PEG 6000
Matthews coefficient: 2.81
Solvent content (%): 56.22
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: 2019-12-04
Crystal structure of an engineered construct of phosphatidylinositol 4 kinase III beta in complex with GTP gamma S loaded Rab11 (PDB entry 5C46)
Macromolecule: Phosphatidylinositol 4-kinase beta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.1.67
Sequence length: 529 residues
Sequence: GSHMQNNSAKQSWLLRLFESKLFDISMAISYLYNSKEPGVQAYIGNRLFCFRNEDVDFYLPQLLNMYIHMDEDVGDAIKPYIVHRCRQSINFSLQCALLLGAYSSDMHISTQRHSRGTKLRKLILSDELKPANLKRTAANPKVENEDEPVRLAPEREFIKSLMAIGKRLATLPTKEQKTQRLISELSLLNHKLPARVWLPTAGFDHHVVRVPHTQAVVLNSKDKAPYLIYVEVLECENFDTTSVPARIPENRRDPEDPSAVALKEPWQEKVRRIREGSPYGHLPNWRLLSVIVKCGDDLRQELLAFQVLKQLQSIWEQERVPLWIKPYKILVISADSGMIEPVVNAVSIHQVKKQSQLSLLDYFLQEHGSYTTEAFLSAQRNFVQSCAGYCLVCYLLQVKDRHNGNILLDAEGHIIHIDFGFILSSSPRNLGFETSAFKLTTEFVDVMGGLDGDMFNYYKMLMLQGLIAARKHMDKVVQIVEIMQQGSQLPCFHGSSTIRNLKERFHMSMTEEQLQLLVEQMVDGSMRS
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.65
R work: 0.2161
R free: 0.2461
Average B factor: 82.1371
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.6
Crystallization temperature (K): 290
Crystal growth procedure: PEG-4000, sodium citrate, ammonium sulfate, glycerol
Matthews coefficient: 2.67
Solvent content (%): 53.99
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: 2016-01-20