satarupa22/MacromolecularLigandDB huggingface dataset:
TGF-BETA RECEPTOR TYPE 1 KINASE DOMAIN (T204D) (PDB entry 5E8T)
Macromolecule: TGF-beta receptor type-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.30
Sequence length: 307 residues
Sequence: GHMTIARDIVLQESIGKGRFGEVWRGKWRGEEVAVKIFSSREERSWFREAEIYQTVMLRHENILGFIAADNKDNGTWTQLWLVSDYHEHGSLFDYLNRYTVTVEGMIKLALSTASGLAHLHMEIVGTQGKPAIAHRDLKSKNILVKKNGTCCIADLGLAVRHDSATDTIDIAPNHRVGTKRYMAPEVLDDSINMKHFESFKRADIYAMGLVFWEIARRCSIGGIHEDYQLPYYDLVPSDPSVEEMRKVVCEQKLRPNIPNRWQSCEALRVMAKIMRECWYANGAARLTALRIKKTLSQLSQQEGIKM
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.1686
R free: 0.1895
Average B factor: 22.29
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.6
Crystallization temperature (K): 277
Crystal growth procedure: 23%(w/v) PEG3350, 3%(v/v) glcyerol
Matthews coefficient: 2.05
Solvent content (%): 40.11
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: 2016-05-11
CRYSTAL STRUCTURE OF MONOBODY GG3/ABL1 SH2 DOMAIN COMPLEX (PDB entry 5DC0)
Macromolecule: Fibronectin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 93 residues
Sequence: VSDVPTKLEVVAATPTSLLISWDAPAVTVVHYVITYGETGGNSPVQEFTVPGSKSTATISGLSPGVDYTITVYALLSSSHWVYESPISINYRT
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.23
R work: 0.19129
R free: 0.24386
Average B factor: 25.722
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 291
Crystal growth procedure: 0.1M sodium tartrate pH=8 and 25% w/v polyethylene glycol 3350
Matthews coefficient: 2.04
Solvent content (%): 39.82
Release date: 2016-03-02
CRYSTAL STRUCTURE OF HUMAN FKBP51 FK1 DOMAIN A19T MUTANT IN COMPLEX WITH 2-PYRIDONE (PDB entry 6TX4)
Macromolecule: Peptidyl-prolyl cis-trans isomerase FKBP5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 128 residues
Sequence: GAPATVTEQGEDITSKKDRGVLKIVKRVGNGEETPMIGDKVYVHYKGKLSNGKKFDSSHDRNEPFVFSLGKGQVIKAWDIGVATMKKGEICHLLCKPEYAYGSAGSLPKIPSNATLFFEIELLDFKGE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.06
R work: 0.1131
R free: 0.1298
Average B factor: 15.94
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293.15
Crystal growth procedure: 28-41% PEG3350, 0.2 M NH4OAc, 0.1 M HEPES
Matthews coefficient: 2.33
Solvent content (%): 47.25
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: 2020-05-27
ITK kinase domain in complex with inhibitor compound (PDB entry 4QD6)
Macromolecule: Tyrosine-protein kinase ITK/TSK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 266 residues
Sequence: GSVIDPSELTFVQEIGSGQFGLVHLGYWLNKDKVAIKTIREGAMSEEDFIEEAEVMMKLSHPKLVQLYGVCLEQAPICLVFEFMEHGCLSDYLRTQRGLFAAETLLGMCLDVCEGMAYLEEACVIHRDLAARNCLVGENQVIKVSDFGMTRFVLDDQETSSTGTKFPVKWASPEVFSFSRYSSKSDVWSFGVLMWEVFSEGKIPYENRSNSEVVEDISTGFRLYKPRLASTHVYQIMNHCWKERPEDRPAFSRLLRQLAEIAESGL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.45
R work: 0.20861
R free: 0.26689
Average B factor: 56.672
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.2M Sodium Nitrate, 0.1M Bis Tris propane, 20% PEG 3350, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Matthews coefficient: 2.44
Solvent content (%): 49.67
Ligand: trans-4-({6-[(5-phenyl-1H-pyrazol-3-yl)amino]-4-(phenylsulfonyl)pyridin-2-yl}amino)cyclohexanol (30T)
Ligand formula: C26 H27 N5 O3 S
Ligand molecular weight: 489.589
Ligand SMILES: c1ccc(cc1)c2cc(n[nH]2)Nc3cc(cc(n3)NC4CCC(CC4)O)S(=O)(=O)c5ccccc5
Ligand InChI: InChI=1S/C26H27N5O3S/c32-20-13-11-19(12-14-20)27-24-15-22(35(33,34)21-9-5-2-6-10-21)16-25(28-24)29-26-17-23(30-31-26)18-7-3-1-4-8-18/h1-10,15-17,19-20,32H,11-14H2,(H3,27,28,29,30,31)/t19-,20-
Release date: 2015-01-14
Human CSNK2A2 bound to ERB-041 (PDB entry 6QY8)
Macromolecule: Casein kinase II subunit alpha'
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 336 residues
Sequence: SMPGPAAGSRARVYAEVNSLRSREYWDYEAHVPSWGNQDDYQLVRKLGRGKYSEVFEAINITNNERVVVKILKPVKKKKIKREVKILENLRGGTNIIKLIDTVKDPVSKTPALVFEYINNTDFKQLYQILTDFDIRFYMYELLKALDYCHSKGIMHRDVKPHNVMIDHQQKKLRLIDWGLAEFYHPAQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRREPFFHGQDNYDQLVRIAKVLGTEELYGYLKKYHIDLDPHFNDILGQHSRKRWENFIHSENRHLVSPEALDLLDKLLRYDHQQRLTAKEAMEHPYFYPVVKEQSQP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.26321
R free: 0.29116
Average B factor: 15.532
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 20% (w/v) PEG10000, 0.1M HEPES pH 7.5
Matthews coefficient: 2.23
Solvent content (%): 44.91
Ligand: 2-(3-FLUORO-4-HYDROXYPHENYL)-7-VINYL-1,3-BENZOXAZOL-5-OL (041)
Ligand formula: C15 H10 F N O3
Ligand molecular weight: 271.243
Ligand SMILES: C=Cc1cc(cc2c1oc(n2)c3ccc(c(c3)F)O)O
Ligand InChI: InChI=1S/C15H10FNO3/c1-2-8-5-10(18)7-12-14(8)20-15(17-12)9-3-4-13(19)11(16)6-9/h2-7,18-19H,1H2
Release date: 2020-03-25
Crystal Structure of the Tyrosine Kinase Domain of FGF Receptor 2 harboring an E565A/K659M Double Gain-of-Function Mutation (PDB entry 5UI0)
Macromolecule: Fibroblast growth factor receptor 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 324 residues
Sequence: MGSSHHHHHHSQDPMLAGVSEYELPEDPKWEFPRDKLTLGKPLGEGAFGQVVMAEAVGIDKDKPKEAVTVAVKMLKDDATEKDLSDLVSEMEMMKMIGKHKNIINLLGACTQDGPLYVIVAYASKGNLREYLRARRPPGMEYSYDINRVPEEQMTFKDLVSCTYQLARGMEYLASQKCIHRDLAARNVLVTENNVMKIADFGLARDINNIDYYKMTTNGRLPVKWMAPEALFDRVYTHQSDVWSFGVLMWEIFTLGGSPYPGIPVEELFKLLKEGHRMDKPANCTNELYMMMRDCWHAVPSQRPTFKQLVEDLDRILTLTTNEE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.05
R work: 0.1822
R free: 0.2067
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 25 mM HEPES pH 7.5, 15%-25% w/v PEG 4000, 0.2-0.3 M Ammonium Sulfate
Matthews coefficient: 2.87
Solvent content (%): 57.16
Ligand: CITRATE ANION (FLC)
Ligand formula: C6 H5 O7
Ligand molecular weight: 189.1
Ligand SMILES: C(C(=O)[O-])C(CC(=O)[O-])(C(=O)[O-])O
Ligand InChI: InChI=1S/C6H8O7/c7-3(8)1-6(13,5(11)12)2-4(9)10/h13H,1-2H2,(H,7,8)(H,9,10)(H,11,12)/p-3
Release date: 2017-02-22
Structure of Optineurin bound to HOIP NZF1 domain and M1-linked diubiquitin, crystal form 2 (PDB entry 9B0Z)
Macromolecule: Optineurin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 96 residues
Sequence: GPDRAVLKELSEKLELAEKALASKQLQMDEMKQTIAKQEEDLETMTILRAQMEVYCSDFHAERAAREKIHEEKEQLALQLAVLLKENDAFEDGGRQ
Oligomeric state: Hetero 7-mer
Stoichiometry: A2, B2, C2, D1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.41
R work: 0.2208
R free: 0.2695
Average B factor: 71.98
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 20% PEG 2K MME, 0.2 M TAO and 0.1 M Tris pH 8.5. Cryoprotected in mother liquor containing 20% glycerol
Matthews coefficient: 3.53
Solvent content (%): 65.14
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: 2024-07-31
KRas G12C in complex with Compound 7b (PDB entry 7YCE)
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: GMTEYKLVVVGACGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKSDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.2737
R free: 0.291
Average B factor: 25.494
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: MES, ammonium sulfate, PEG550MME
Matthews coefficient: 2.67
Solvent content (%): 53.89
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: 2022-08-10
Crystal structure of human secreted phospholipase A2 group IIE with LY311727 (PDB entry 5WZW)
Macromolecule: Group IIE secretory phospholipase A2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.1.4
Sequence length: 123 residues
Sequence: NLVQFGVMIEKMTGKSALQYNDYGCYCGIGGSHWPVDQTDWCCHAHDCCYGRLEKLGCEPKLEKYLFSVSERGIFCAGRTTCQRLTCECDKRAALCFRRNLGTYNRKYAHYPNKLCTGPTPPC
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.95
R work: 0.2042
R free: 0.2552
Average B factor: 19.838
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 277
Crystal growth procedure: 2.2M Sodium chloride, 0.1M BIS-TRIS propane pH 7.0
Matthews coefficient: 3.39
Solvent content (%): 63.67
Ligand: (3-{[3-(2-amino-2-oxoethyl)-1-benzyl-2-ethyl-1H-indol-5-yl]oxy}propyl)phosphonic acid (U8D)
Ligand formula: C22 H27 N2 O5 P
Ligand molecular weight: 430.434
Ligand SMILES: CCc1c(c2cc(ccc2n1Cc3ccccc3)OCCCP(=O)(O)O)CC(=O)N
Ligand InChI: InChI=1S/C22H27N2O5P/c1-2-20-19(14-22(23)25)18-13-17(29-11-6-12-30(26,27)28)9-10-21(18)24(20)15-16-7-4-3-5-8-16/h3-5,7-10,13H,2,6,11-12,14-15H2,1H3,(H2,23,25)(H2,26,27,28)
Release date: 2018-01-24
Thrombin in complex with (2R)-2-(benzylsulfonylamino)-N-(2-((4- carbamimidoylphenyl)methylamino)-2-oxo-ethyl)-N-methyl-3-phenyl- propanamide (PDB entry 4UFF)
Macromolecule: THROMBIN HEAVY CHAIN
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.5
Sequence length: 258 residues
Sequence: IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQFG
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.55
R work: 0.16
R free: 0.1874
Average B factor: 22.9
Crystallization pH: 7.5
Crystal growth procedure: SEE MATERIALS AND METHODS SECTION OF PUBLICATION, pH 7.5
Matthews coefficient: 2.5
Solvent content (%): 50.71
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2016-01-27
PTP1B P206G mutation, open state (PDB entry 7MNE)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 308 residues
Sequence: GHMASMEMEKEFEQIDKSGSWAAIYQDIRHEASDFPCRVAKLPKNKNRNRYRDVSPFDHSRIKLHQEDNDYINASLIKMEEAQRSYILTQGPLPNTCGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQKEEKEMIFEDTNLKLTLISEDIKSYYTVRQLELENLTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRESGSLSGEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKDPSSVDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFIMGDSSVQDQWKELSHEDLEPHN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.1632
R free: 0.1761
Average B factor: 24.86
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.2 M MgCl2, 0.1 M Tris pH 7.8, 17% PEG
Matthews coefficient: 2.27
Solvent content (%): 45.79
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: 2022-05-18
Crystal structure of IRE1a in complex with G-4100 (PDB entry 6XDF)
Macromolecule: Serine/threonine-protein kinase/endoribonuclease IRE1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 431 residues
Sequence: GSSPSLEQDDGDEETSVVIVGKISFCPKDVLGHGAEGTIVYRGMFDNRDVAVKRILPECFSFADREVQLLRESDEHPNVIRYFCTEKDRQFQYIAIELCAATLQEYVEQKDFAHLGLEPITLLQQTTSGLAHLHSLNIVHRDLKPHNILISMPNAHGKIKAMISDFGLCKKLAVGRHSFSRRSGVPGTEGWIAPEMLSEDCKENPTYTVDIFSAGCVFYYVISEGSHPFGKSLQRQANILLGACSLDCLHPEKHEDVIARELIEKMIAMDPQKRPSAKHVLKHPFFWSLEKQLQFFQDVSDRIEKESLDGPIVKQLERGGRAVVKMDWRENITVPLQTDLRKFRTYKGGSVRDLLRAMRNKKHHYRELPAEVRETLGSLPDDFVCYFTSRFPHLLAHTYRAMELCSHERLFQPYYFHEPPEPQPPVTPDAL
Oligomeric state: Homo 2-mer
Stoichiometry: A2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.54
R work: 0.207
R free: 0.2627
Average B factor: 61.138
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 10% (v/v) isopropanol, 11% (w/v) PEG4000, 0.1 M Na-citrate, pH 5.6
Matthews coefficient: 3.06
Solvent content (%): 59.85
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2021-04-21
X-ray structure of furin (PCSK3) in complex with benzamidine (PDB entry 8B4V)
Macromolecule: Furin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.75
Sequence length: 480 residues
Sequence: DVYQEPTDPKFPQQWYLSGVTQRDLNVKAAWAQGYTGHGIVVSILDDGIEKNHPDLAGNYDPGASFDVNDQDPDPQPRYTQMNDNRHGTRCAGEVAAVANNGVCGVGVAYNARIGGVRMLDGEVTDAVEARSLGLNPNHIHIYSASWGPEDDGKTVDGPARLAEEAFFRGVSQGRGGLGSIFVWASGNGGREHDSCNCDGYTNSIYTLSISSATQFGNVPWYSEACSSTLATTYSSGNQNEKQIVTTDLRQKCTESHTGTSASAPLAAGIIALTLEANKNLTWRDMQHLVVQTSKPAHLNANDWATNGVGRKVSHSYGYGLLDAGAMVALAQNWTTVAPQRKCIIDILTEPKDIGKRLEVRKTVTACLGEPNHITRLEHAQARLTLSYNRRGDLAIHLVSPMGTRSTLLAARPHDYSADGFNDWAFMTTHSWDEDPSGEWVLEIENTSEANNYGTLTKFTLVLYGTASGSLVPRGSHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.1535
R free: 0.1658
Average B factor: 26.89
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293.15
Crystal growth procedure: CRYSTALLIZATION SOLUTION: 100mM MES, 200mM K/NAH2PO4, PH 5.5, 2 M NACL; RESERVOIR SOLUTION: 3.0-3.2M NACL
Matthews coefficient: 3.75
Solvent content (%): 67.16
Ligand: BENZAMIDINE (BEN)
Ligand formula: C7 H8 N2
Ligand molecular weight: 120.152
Ligand SMILES: [H]N=C(c1ccccc1)N
Ligand InChI: InChI=1S/C7H8N2/c8-7(9)6-4-2-1-3-5-6/h1-5H,(H3,8,9)
Release date: 2023-10-04
Crystal structure of VEGFR-2 domains 4-5 in complex with DARPin D4b (PDB entry 5OYJ)
Macromolecule: DARPin D4b
Type: Protein, polypeptide(L)
Source organism: synthetic construct
Sequence length: 169 residues
Sequence: MRGSHHHHHHGSDLGKKLLEAARAGQDDEVRILMANGADVNAHDQNGFTPLHLAAWYGHLEIVGVLLKNGADVNAFDKYGFTPLHLAAEEGHLEVVEVLLKYGADVNAKDEHGSTPLHLAADIGHLEIVEVLLKNGADVNAQDKFGKTAFDISIDNGNEDLAEILQKLN
Oligomeric state: Hetero 4-mer
Stoichiometry: A2, B2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.38
R work: 0.1779
R free: 0.2288
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.4
Crystallization temperature (K): 293.15
Crystal growth procedure: 0.2 M calcium acetate monohydrate, 15% PEG 4000, 0.1 M sodium cacodylate pH 6.4, cryoprotected with 15% trehalose
Matthews coefficient: 3.64
Solvent content (%): 66.25
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: 2018-03-14
Structure of Cyclophilin A in complex with Saccharin. (PDB entry 4N1O)
Macromolecule: Peptidyl-prolyl cis-trans isomerase A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 165 residues
Sequence: MVNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFGSRNGKTSKKITIADCGQLE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.75
R work: 0.17901
R free: 0.22147
Average B factor: 29.161
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 277
Crystal growth procedure: Tris, PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Matthews coefficient: 2.73
Solvent content (%): 54.87
Ligand: 1,2-BENZISOTHIAZOL-3(2H)-ONE 1,1-DIOXIDE (LSA)
Ligand formula: C7 H5 N O3 S
Ligand molecular weight: 183.184
Ligand SMILES: c1ccc2c(c1)C(=O)NS2(=O)=O
Ligand InChI: InChI=1S/C7H5NO3S/c9-7-5-3-1-2-4-6(5)12(10,11)8-7/h1-4H,(H,8,9)
Release date: 2015-08-12
Structure of the activation intermediate of cathepsin K in complex with the 3-cyano-3-aza-beta-amino acid inhibitor Gu2602 (PDB entry 7QBM)
Macromolecule: Cathepsin K
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.22.38
Sequence length: 216 residues
Sequence: RAPDSVDYRKKGYVTPVKNQGQCGSCWAFSSVGALEGQLKKKTGKLLNLSPQNLVDCVSENDGCGGGYMTNAFQYVQKNRGIDSEDAYPYVGQEESCMYNPTGKAAKCRGYREIPEGNEKALKRAVARVGPVSVAIDASLTSFQFYSKGVYYDESCNSDNLNHAVLAVGYGIQKGNKHWIIKNSWGENWGNKGYILMARNKNNACGIANLASFPKM
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.88
R work: 0.1904
R free: 0.234
Average B factor: 34.616
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 290
Crystal growth procedure: 10% PEG 8000, 20% ethylene glycol, 0.02 M sodium formate, 0.02 M ammonium acetate, 0.02 M trisodium citrate, 0.02 M sodium potassium L-tartrate, 0.02 M sodium oxamate, 0.1 M MES/imidazole pH 6.5
Matthews coefficient: 2.1
Solvent content (%): 41.38
Ligand: ~{tert}-butyl ~{N}-[iminomethyl-[2-[methyl-(phenylmethyl)amino]-2-oxidanylidene-ethyl]amino]carbamate (A0U)
Ligand formula: C16 H24 N4 O3
Ligand molecular weight: 320.387
Ligand SMILES: CC(C)(C)OC(=O)NN(CC(=O)N(C)Cc1ccccc1)C=N
Ligand InChI: InChI=1S/C16H24N4O3/c1-16(2,3)23-15(22)18-20(12-17)11-14(21)19(4)10-13-8-6-5-7-9-13/h5-9,12,17H,10-11H2,1-4H3,(H,18,22)/b17-12+
Release date: 2022-01-26
Crystal Structure of Human Myt1 Kinase domain Bounded with compound 8f (PDB entry 8ZUD)
Macromolecule: Membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 287 residues
Sequence: HQLQPRRVSFRGEASETLQSPGYDPSRPESFFQQSFQRLSRLGHGSYGEVFKVRSKEDGRLYAVKRSMSPFRGPKDRARKLAEVGSHEKVGQHPCCVRLEQAWEEGGILYLQTELCGPSLQQHCEAWGASLPEAQVWGYLRDTLLALAHLHSQGLVHLDVKPANIFLGPRGRCKLGDFGLLVELGTAGAGEVQEGDPRYMAPELLQGSYGTAADVFSLGLTILEVACNMELPHGGEGWQQLRQGYLPPEFTAGLSSELRSVLVMMLEPDPKLRATAEALLALPVLRQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.5051008788
R work: 0.202858375722
R free: 0.237756545815
Average B factor: 32.4496558341
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.8 M Ammonium sulfate,100 mM 
Sodium citrate,pH 6.5
Matthews coefficient: 2.55
Solvent content (%): 51.7
Ligand: 2-azanyl-3-(2,6-dimethyl-3-oxidanyl-phenyl)-5-(2-morpholin-4-ylpyridin-4-yl)benzamide (A1D82)
Ligand formula: C24 H26 N4 O3
Ligand molecular weight: 418.488
Ligand SMILES: Cc1ccc(c(c1c2cc(cc(c2N)C(=O)N)c3ccnc(c3)N4CCOCC4)C)O
Ligand InChI: InChI=1S/C24H26N4O3/c1-14-3-4-20(29)15(2)22(14)18-11-17(12-19(23(18)25)24(26)30)16-5-6-27-21(13-16)28-7-9-31-10-8-28/h3-6,11-13,29H,7-10,25H2,1-2H3,(H2,26,30)
Release date: 2024-09-11
STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE (RT) TERNARY COMPLEX WITH A DOUBLE STRANDED DNA AND AN INCOMING D4TTP AT PH 9.0 (PDB entry 6ASW)
Macromolecule: HIV-1 REVERSE TRANSCRIPTASE P66 SUBUNIT
Type: Protein, polypeptide(L)
Source organism: Human immunodeficiency virus type 1 BH10
EC number: 2.7.7.49
Sequence length: 556 residues
Sequence: MVPISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENPYNTPVFACKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFKKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEKDSWTVNDIQKLVGKLNWASQIYPGIKVRQLSKLLRGTKALTEVIPLTEEAELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRETKLGKAGYVTNKGRQKVVPLTNTTNQKTELQAIYLALQDSGLEVNIVTDSQYALGIIQAQPDKSESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSA
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.605
R work: 0.179
R free: 0.22
Average B factor: 94.1117
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 9.5
Crystallization temperature (K): 277
Crystal growth procedure: PEG 8000, NaCl, CHES (N-Cyclohexyl-2-aminoethanesulfonic acid), TRIS, MgCl2, d4T triphosphate
Matthews coefficient: 3.19
Solvent content (%): 61.49
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: 2018-08-15
ERK2 mini-fragment binding (PDB entry 6QAW)
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): 1.84
R work: 0.174
R free: 0.221
Average B factor: 30.412
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.2
Crystallization temperature (K): 293
Crystal growth procedure: 0.2M (NH4)2SO4
34% MPEG 2000
0.02M Mercaptoethanol
0.1M pH=7.2 HEPES/NaOH
Matthews coefficient: 2.3
Solvent content (%): 46.56
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: 2019-03-27
Human Exonuclease 5 crystal structure in complex with a ssDNA (PDB entry 7LW8)
Macromolecule: Exonuclease V
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1
Sequence length: 346 residues
Sequence: SNALEDAQESKALVNMPGPSSESLGKDDKPISLQNWKRGLDILSPMERFHLKYLYVTDLATQNWCELQTAYGKELPGFLAPEKAAVLDTGASIHLARELELHDLVTVPVTTKEDAWAIKFLNILLLIPTLQSEGHIREFPVFGEVEGVLLVGVIDELHYTAKGELELAELKTRRRPMLPLEAQKKKDCFQVSLYKYIFDAMVQGKVTPASLIHHTKLCLEKPLGPSVLRHAQQGGFSVKSLGDLMELVFLSLTLSDLPVIDILKIEYIHQETATVLGTEIVAFKEKEVRAKVQHYMAYWMGHREPQGVDVEEAWKCRTCTYADICEWRKGSGVLSSTLAPQVKKAK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.88
R work: 0.2046
R free: 0.2586
Average B factor: 39.7004
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 16% PEG 3350 and 0.2 M lithium acetate
Matthews coefficient: 2.44
Solvent content (%): 49.55
Ligand: IRON/SULFUR CLUSTER (SF4)
Ligand formula: Fe4 S4
Ligand molecular weight: 351.64
Ligand SMILES: [S]12[Fe]3[S]4[Fe]1[S]5[Fe]2[S]3[Fe]45
Ligand InChI: InChI=1S/4Fe.4S
Release date: 2021-07-14