satarupa22/MacromolecularLigandDB huggingface dataset:
Human Xylosyltransferase 1 in complex with peptide QEEEYSGGGQGG (PDB entry 6EJA)
Macromolecule: Xylosyltransferase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.2.26
Sequence length: 751 residues
Sequence: APLVHHHHHHALDENLYFQGALADVSRPPHARKTGGSSPETKYDQPPKCDISGKEAISALSRAKSKHCRQEIGETYCRHKLGLLMPEKVTRFCPLEGKANKNVQWDEDSVEYMPANPVRIAFVLVVHGRASRQLQRMFKAIYHKDHFYYIHVDKRSNYLHRQVLQVSRQYSNVRVTPWRMATIWGGASLLSTYLQSMRDLLEMTDWPWDFFINLSAADYPIRTNDQLVAFLSRYRDMNFLKSHGRDNARFIRKQGLDRLFLECDAHMWRLGDRRIPEGIAVDGGSDWFLLNRRFVEYVTFSTDDLVTKMKQFYSYTLLPAESFFHTVLENSPHCDTMVDNNLRITNWNRKLGCKCQYKHIVDWCGCSPNDFKPQDFHRFQQTARPTFFARKFEAVVNQEIIGQLDYYLYGNYPAGTPGLRSYWENVYDEPDGIHSLSDVTLTLYHSFARLGLRRAETSLHTDGENSCRYYPMGHPASVHLYFLADRFQGFLIKHHATNLAVSKLETLETWVMPKKVFKIASPPSDFGRLQFSEVGTDWDAKERLFRNFGGLLGPMDEPVGMQKWGKGPNVTVTVIWVDPVNVIAATYDILIESTAEFTHYKPPLNLPLRPGVWTVKILHHWVPVAETKFLVAPLTFSNRQPIKPEEALKLHNGPLRNAYMEQSFQSLNPVLSLPINPAQVEQARRNAASTGTALEGWLDSLVGGMWTAMDICATGPTACPVMQTCSQTAWSSFSPDPKSELGAVKPDGRLR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.94
R work: 0.1844
R free: 0.2125
Average B factor: 56.5414
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 55-65% Morpheus Precipitant mix 2 (PEG8000 and Ethylene glycol)
0.1M Bicine/Tris buffer at pH 7.5
0.1M of NPS mix (0.033M of each)
Matthews coefficient: 2.48
Solvent content (%): 50.35
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2018-05-02
Crystal structure of the human YTHDC2 YTH domain (PDB entry 6K6U)
Macromolecule: 3'-5' RNA helicase YTHDC2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.4.13
Sequence length: 143 residues
Sequence: GHMPVRYFIMKSSNLRNLEISQQKGIWSTTPSNERKLNRAFWESSIVYLVFSVQGSGHFQGFSRMSSEIGREKSQDWGSAGLGGVFKVEWIRKESLPFQFAHHLLNPWNDNKKVQISRDGQELEPLVGEQLLQLWERLPLGEK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.27
R work: 0.1952
R free: 0.2459
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: Tacsimate,Tris,PEG 3350
Matthews coefficient: 2.2
Solvent content (%): 44.21
Release date: 2019-12-25
Truncated mitofusin-1, nucleotide-free (PDB entry 5GO4)
Macromolecule: Mitofusin-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5
Sequence length: 433 residues
Sequence: GPHMGGSMAEPVSPLKHFVLAKKAITAIFDQLLEFVTEGSHFVEATYKNPELDRIATEDDLVEMQGYKDKLSIIGEVLSRRHMKVAFFGRTSSGKSSVINAMLWDKVLPSGIGHITNCFLSVEGTDGDKAYLMTEGSDEKKSVKTVNQLAHALHMDKDLKAGCLVRVFWPKAKCALLRDDLVLVDSPGTDVTTELDSWIDKFCLDADVFVLVANSESTLMNTEKHFFHKVNERLSKPNIFILNNRWDASASEPEYMEDVRRQHMERCLHFLVEELKVVNALEAQNRIFFVSAKEVLSARKQKAQGMPESGVALAEGFHARLQEFQNFEQIFEECISQSAVKTKFEQHTIRAKQILATVKNIMDSVNLAAEDKSAASAASAASAASAAARLPKEIDQLEKIQNNSKLLRNKAVQLENELENFTKQFLPSSNEES
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.202
R work: 0.1751
R free: 0.2139
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.2M sodium citrate tribasic dehydrate and 20~22% PEG3350
Matthews coefficient: 3.46
Solvent content (%): 64.47
Release date: 2017-01-25
Binding and Enhanced Binding between Key Immunity Proteins TRAF6 and TIFA (PDB entry 5ZUJ)
Macromolecule: TNF receptor-associated factor 6
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.27
Sequence length: 161 residues
Sequence: MNGIYIWKIGNFGMHLKCQEEEKPVVIHSPGFYTGKPGYKLCMRLHLQLPTAQRCANYISLFVHTMQGEYDSHLPWPFQGTIRLTILDQSEAPVRQNHEEIMDAKPELLAFQRPTIPRNPKGFGYVTFMHLEALRQRTFIKDDTLLVRCEVSTLEHHHHHH
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.6
R work: 0.1929
R free: 0.2416
Average B factor: 46.2
Crystallization method: EVAPORATION
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M HEPES sodium, pH 7.5, 1M Sodium citrate tribasic dihydrate, 10 mM TCEP
Matthews coefficient: 3.14
Solvent content (%): 60.79
Release date: 2018-12-05
Fragment-based screening of HSP70 sheds light on the functional role of ATP-binding site residues (PDB entry 5AQY)
Macromolecule: HEAT SHOCK 70 KDA PROTEIN 1A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.3.51
Sequence length: 394 residues
Sequence: GPLGSMAKAAAIGIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDTERLIGDAAKNQVALNPQNTVFDAKRLIGRKFGDPVVQSDMKHWPFQVINDGDKPKVQVSYKGETKAFYPEEISSMVLTKMKEIAEAYLGYPVTNAVITVPAYFNDSQRQATKDAGVIAGLNVLRIINEPTAAAIAYGLDRTGKGERNVLIFDLGGGTFDVSILTIDDGIFEVKATAGDTHLGGEDFDNRLVNHFVEEFKRKHKKDISQNKRAVRRLRTACERAKRTLSSSTQASLEIDSLFEGIDFYTSITRARFEELCSDLFRSTLEPVEKALRDAKLDKAQIHDLVLVGGSTRIPKVQKLLQDFFNGRDLNKSINPDEAVAYGAAVQAAILIKSTRAAAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.56
R work: 0.174
R free: 0.2036
Average B factor: 28.08
Crystallization pH: 7.5
Crystal growth procedure: 17-28% (W/V) PEG3350, 0.1M HEPES PH 7.5, 2MM MGCL2, 2MM NAH2PO4 AND 5MM ADENOSINE
Matthews coefficient: 2.4
Solvent content (%): 48.8
Ligand: ADENOSINE (ADN)
Ligand formula: C10 H13 N5 O4
Ligand molecular weight: 267.241
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CO)O)O)N
Ligand InChI: InChI=1S/C10H13N5O4/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(18)6(17)4(1-16)19-10/h2-4,6-7,10,16-18H,1H2,(H2,11,12,13)/t4-,6-,7-,10-/m1/s1
Release date: 2016-10-05
A subcomplex crystal structure of human cytosolic aspartyl-tRNA synthetase and heterotetrameric glutathione transferase-homology domains in multi-tRNA synthetase complex (PDB entry 5Y6L)
Macromolecule: Methionine--tRNA ligase, cytoplasmic
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.1.1.10
Sequence length: 232 residues
Sequence: MRLFVSDGVPGCLPVLAAAGRARGRAEVLISTVGPEDCVVPFLTRPKVPVLQLDSGNYLFSTSAICRYFFLLSGWEQDDLTNQWLEWEATELQPALSAALYYLVVQGKKGEDVLGSVRRALTHIDHSLSRQNCPFLAGETESLADIVLWGALYPLLQDPAYLPEELSALHRWFQTLSTQEPCQRAAETVLKQQGVLALRPYLQKQPQPSPAEGRAVTNEPEEEELEHHHHHH
Oligomeric state: Hetero 5-mer
Stoichiometry: A1, B1, C1, D1, E1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.9
R work: 0.1765
R free: 0.2518
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293.15
Crystal growth procedure: 10% PEG 3000
Na/K phosphate pH 6.2
Matthews coefficient: 1.72
Solvent content (%): 28.3
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: 2018-08-15
Structure of human PARG complexed with PARG-292 (PDB entry 7KG7)
Macromolecule: Poly(ADP-ribose) glycohydrolase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.1.143
Sequence length: 531 residues
Sequence: GSSPDKKWLGTPIEEMRRMPRCGIRLPLLRPSANHTVTIRVDLLRAGEVPKPFPTHYKDLWDNKHVKMPCSEQNLYPVEDENGERTAGSRWELIQTALLNKFTRPQNLKDAILKYNVAYSKKWDFTALIDFWDKVLEEAEAQHLYQSILPDMVKIALCLPNICTQPIPLLAAAMNHSITMSQEQIASLLANAFFCTFPRRNAKMKSEYSSYPDINFNRLFEGRSSRKPEKLKTLFCYFRRVTAAAPTGLVTFTRQSLEDFPEWERCEKPLTRLHVTYEGTIEENGQGMLQVDFANRFVGGGVTSAGLVQEEIRFLINPELIISRLFTEVLDHNECLIITGTEQYSEYTGYAETYRWSRSHEDGSERDDWQRRCTEIVAIDALHFRRYLDQFVPEKMRRELNKAYCGFLRPGVSSENLSAVATGNWGCGAFGGDARLKALIQILAAAAAERDVVYFTFGDSELMRDIYSMHIFLTERKLTVGDVYKLLLRYYNEECRNCSTPGPDIKLYPFIYHAVESCAETADHSGQRTGT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.85
R work: 0.1774
R free: 0.1955
Average B factor: 36.36
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 295
Crystal growth procedure: 0.1 M PCTP, pH 7.5, 0.2 M AmSO4, 18-23% PEG3350
Matthews coefficient: 2.35
Solvent content (%): 47.8
Ligand: 8-{[2-(1,1-dioxo-1lambda~6~,4-thiazinan-4-yl)ethyl]sulfanyl}-1,3-dimethyl-3,7-dihydro-1H-purine-2,6-dione (WDJ)
Ligand formula: C13 H19 N5 O4 S2
Ligand molecular weight: 373.451
Ligand SMILES: CN1c2c([nH]c(n2)SCCN3CCS(=O)(=O)CC3)C(=O)N(C1=O)C
Ligand InChI: InChI=1S/C13H19N5O4S2/c1-16-10-9(11(19)17(2)13(16)20)14-12(15-10)23-6-3-18-4-7-24(21,22)8-5-18/h3-8H2,1-2H3,(H,14,15)
Release date: 2021-03-10
CRYSTAL STRUCTURE OF BACE-1 IN COMPLEX WITH {(1R,2R)-2-[(R)-2-Amino-4-(4-difluoromethoxy-phenyl)-4,5-dihydro-oxazol-4-yl]-cyclopropyl}-(5-chloro-pyridin-3-yl)-methanone (PDB entry 5EZX)
Macromolecule: Beta-secretase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.23.46
Sequence length: 390 residues
Sequence: RGSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVASIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.20816
R free: 0.2364
Average B factor: 33.623
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 2.5M SODIUM FORMATE, 100MM HEPES
Matthews coefficient: 3.07
Solvent content (%): 59.99
Ligand: DIMETHYL SULFOXIDE (DMS)
Ligand formula: C2 H6 O S
Ligand molecular weight: 78.133
Ligand SMILES: CS(=O)C
Ligand InChI: InChI=1S/C2H6OS/c1-4(2)3/h1-2H3
Release date: 2016-02-24
Crystal Structure of CK2alpha with N-(3-(((2-chloro-[1,1'-biphenyl]-4-yl)methyl)amino)propyl)methanesulfonamide bound (PDB entry 5MOE)
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): 1.89
R work: 0.1968
R free: 0.2084
Average B factor: 55.24
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 (%): 44.49
Ligand: ADENOSINE-5'-DIPHOSPHATE (ADP)
Ligand formula: C10 H15 N5 O10 P2
Ligand molecular weight: 427.201
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
Ligand InChI: InChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
Release date: 2017-05-24
REV1 UBM2 domain complex with ubiquitin (PDB entry 6ASR)
Macromolecule: Ubiquitin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 76 residues
Sequence: MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.356
R work: 0.2008
R free: 0.2291
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6
Crystallization temperature (K): 291
Crystal growth procedure: 0.1 M MES pH 6.0, 10 % PEG 8000
Matthews coefficient: 4.14
Solvent content (%): 70.29
Ligand: NICKEL (II) ION (NI)
Ligand formula: Ni
Ligand molecular weight: 58.693
Ligand SMILES: [Ni+2]
Ligand InChI: InChI=1S/Ni/q+2
Release date: 2018-06-20
Carbonic Anhydrase VII Sultam Based Inhibitors (PDB entry 7P1A)
Macromolecule: Carbonic anhydrase 7
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 274 residues
Sequence: MGMTGHHGWGYGQDDGPSHWHKLYPIAQGDRQSPINIISSQAVYSPSLQPLELSYEACMSLSITNNGHSVQVDFNDSDDRTVVTGGPLEGPYRLKQFHFHWGKKHDVGSEHTVDGKSFPSELHLVHWNAKKYSTFGEAASAPDGLAVVGVFLETGDEHPSMNRLTDALYMVRFKGTKAQFSCFNPKSLLPASRHYWTYPGSLTTPPLSESVTWIVLREPISISERQMGKFRSLLFTSEDDERIHMVNNFRPPQPLKGRVVKASFRALEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.58
R work: 0.1892
R free: 0.2062
Average B factor: 17.555
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 17% PEG 3350, 0.2 M Ammonium acetate, 0.1 M Tris-HCl (pH 8.5)
Matthews coefficient: 2.14
Solvent content (%): 42.47
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: 2021-11-17
Jak1 with compound 23 (PDB entry 6DBN)
Macromolecule: Tyrosine-protein kinase JAK1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 316 residues
Sequence: GSIMRDINKLEEQNPDIVSEKKPATEVDPTHFEKRFLKRIRDLGEGHFGKVELCRYDPEGDNTGEQVAVKSLKPESGGNHIADLKKEIEILRNLYHENIVKYKGICTEDGGNGIKLIMEFLPSGSLKEYLPKNKNKINLKQQLKYAVQICKGMDYLGSRQYVHRDLAARNVLVESEHQVKIGDFGLTKAIETDKEYYTVKDDRDSPVFWYAPECLMQSKFYIASDVWSFGVTLHELLTYCDSDSSPMALFLKMIGPTHGQMTVTRLVNTLKEGKRLPCPPNCPDEVYQLMRKCWEFQPSNRTSFQNLIEGFEALLK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.48
R work: 0.186
R free: 0.2619
Average B factor: 55.89
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 298
Crystal growth procedure: 0.1 M Tris pH 8.5, 6-9% MPD, 24-29% PEG-1500
Matthews coefficient: 2.03
Solvent content (%): 39.5
Ligand: [(1S)-2,2-difluorocyclopropyl][(1R,5S)-3-{2-[(1-methyl-1H-pyrazol-4-yl)amino]pyrimidin-4-yl}-3,8-diazabicyclo[3.2.1]octan-8-yl]methanone (G4J)
Ligand formula: C18 H21 F2 N7 O
Ligand molecular weight: 389.402
Ligand SMILES: Cn1cc(cn1)Nc2nccc(n2)N3CC4CCC(C3)N4C(=O)C5CC5(F)F
Ligand InChI: InChI=1S/C18H21F2N7O/c1-25-8-11(7-22-25)23-17-21-5-4-15(24-17)26-9-12-2-3-13(10-26)27(12)16(28)14-6-18(14,19)20/h4-5,7-8,12-14H,2-3,6,9-10H2,1H3,(H,21,23,24)/t12-,13+,14-/m0/s1
Release date: 2018-08-29
High resolution crystal structure of substrate-free human neprilysin (PDB entry 6GID)
Macromolecule: Neprilysin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.24.11
Sequence length: 696 residues
Sequence: GICKSSDCIKSAARLIQNMDATTEPCTDFFKYACGGWLKRNVIPETSSRYGNFDILRDELEVVLKDVLQEPKTEDIVAVQKAKALYRSCINESAIDSRGGEPLLKLLPDIYGWPVATENWEQKYGASWTAEKAIAQLNSKYGKKVLINLFVGTDDKNSVNHVIHIDQPRLGLPSRDYYECTGIYKEACTAYVDFMISVARLIRQEERLPIDENQLALEMNKVMELEKEIANATAKPEDRNDPMLLYNKMTLAQIQNNFSLEINGKPFSWLNFTNEIMSTVNISITNEEDVVVYAPEYLTKLKPILTKYSARDLQNLMSWRFIMDLVSSLSRTYKESRNAFRKALYGTTSETATWRRCANYVNGNMENAVGRLYVEAAFAGESKHVVEDLIAQIREVFIQTLDDLTWMDAETKKRAEEKALAIKERIGYPDDIVSNDNKLNNEYLELNYKEDEYFENIIQNLKFSQSKQLKKLREKVDKDEWISGAAVVNAFYSSGRNQIVFPAGILQPPFFSAQQSNSLNYGGIGMVIGHEITHGFDDNGRNFNKDGDLVDWWTQQSASNFKEQSQCMVYQYGNFSWDLAGGQHLNGINTLGENIADNGGLGQAYRAYQNYIKKNGEEKLLPGLDLNHKQLFFLNFAQVWCGTYRPEYAVNSIKTDVHSPGNFRIIGTLQNSAEFSEAFHCRKNSYMNPEKKCRVW
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.1899
R free: 0.2354
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 0.2 M potassium nitrate and 20% (w/v) PEG3350
Matthews coefficient: 2.35
Solvent content (%): 47.71
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: 2018-06-27
Inhibitor of MDM2-p53 Interaction (PDB entry 7BMG)
Macromolecule: E3 ubiquitin-protein ligase Mdm2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.27
Sequence length: 98 residues
Sequence: GPLGSSQIPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDAAQQHIVYCSNDLLGDLFGVPSFSVKEHRKIYTMIYRNLVV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.83
R work: 0.229
R free: 0.251
Average B factor: 35.855
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 2.2M (NH4)2SO4
Matthews coefficient: 3.32
Solvent content (%): 62.91
Ligand: (3~{R})-3-(4-chlorophenyl)-2-[(4-ethynylphenyl)methyl]-3-[[1-(hydroxymethyl)cyclopropyl]methoxy]-6-(2-oxidanylpropan-2-yl)isoindol-1-one (U3Z)
Ligand formula: C31 H30 Cl N O4
Ligand molecular weight: 516.027
Ligand SMILES: CC(C)(c1ccc2c(c1)C(=O)N(C2(c3ccc(cc3)Cl)OCC4(CC4)CO)Cc5ccc(cc5)C#C)O
Ligand InChI: InChI=1S/C31H30ClNO4/c1-4-21-5-7-22(8-6-21)18-33-28(35)26-17-24(29(2,3)36)11-14-27(26)31(33,23-9-12-25(32)13-10-23)37-20-30(19-34)15-16-30/h1,5-14,17,34,36H,15-16,18-20H2,2-3H3/t31-/m1/s1
Release date: 2021-04-07
Crystal structure of glucocerebrosidase in complex with allosteric activator (PDB entry 8P41)
Macromolecule: Glucosylceramidase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.1.45
Sequence length: 497 residues
Sequence: ARPCIPKSFGYSSVVCVCNATYCDSFDPPTFPALGTFSRYESTRSGRRMELSMGPIQANHTGTGLLLTLQPEQKFQKVKGFGGAMTDAAALNILALSPPAQNLLLKSYFSEEGIGYNIIRVPMASCDFSIRTYTYADTPDDFQLHNFSLPEEDTKLKIPLIHRALQLAQRPVSLLASPWTSPTWLKTNGAVNGKGSLKGQPGDIYHQTWARYFVKFLDAYAEHKLQFWAVTAENEPSAGLLSGYPFQCLGFTPEHQRDFIARDLGPTLANSTHHNVRLLMLDDQRLLLPHWAKVVLTDPEAAKYVHGIAVHWYLDFLAPAKATLGETHRLFPNTMLFASEACVGSKFWEQSVRLGSWDRGMQYSHSIITNLLYHVVGWTDWNLALNPEGGPNWVRNFVDSPIIVDITKDTFYKQPMFYHLGHFSKFIPEGSQRVGLVASQKNDLDAVALMHPDGSAVVVVLNRSSKDVPLTIKDPAVGFLETISPGYSIHTYLWHRQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.83
R work: 0.2045
R free: 0.2383
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 291
Crystal growth procedure: 2 M (NH4)2SO4, 0.1 M Bis-Tris pH 5.5
Matthews coefficient: 3.22
Solvent content (%): 61.77
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: 2024-03-06
KRASG12C GDP form in complex with Cpd2 (PDB entry 7A1Y)
Macromolecule: GTPase KRas
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 170 residues
Sequence: GMTEYKLVVVGACGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.004
R work: 0.1888
R free: 0.21
Average B factor: 25.63
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: HEPES 100mM - (NH4)2SO4 2.25M - pH7.5
Matthews coefficient: 2.52
Solvent content (%): 51.28
Ligand: ~{N}-(3-bromanyl-2,6-dimethyl-pyridin-4-yl)propanamide (QWH)
Ligand formula: C10 H13 Br N2 O
Ligand molecular weight: 257.127
Ligand SMILES: CCC(=O)Nc1cc(nc(c1Br)C)C
Ligand InChI: InChI=1S/C10H13BrN2O/c1-4-9(14)13-8-5-6(2)12-7(3)10(8)11/h5H,4H2,1-3H3,(H,12,13,14)
Release date: 2021-10-13
Structure of Maternal Embryonic Leucine Zipper Kinase (PDB entry 5TWY)
Macromolecule: Maternal embryonic leucine zipper kinase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 341 residues
Sequence: GSKDYDELLKYYELHETIGTGGFAKVKLACHILTGEMVAIKIMDKNTLGSDLPRIKTEIEALKNLRHQHICQLYHVLETANKIFMVLEYCPGGELFDYIISQDRLSEEETRVVFRQIVSAVAYVHSQGYAHRDLKPENLLFDEYHKLKLIDFGLCAKPKGNKDYHLQTCCGSLAYAAPELIQGKSYLGSEADVWSMGILLYVLMCGFLPFDDDNVMALYKKIMRGKYDVPKWLSPSSILLLQQMLQVDPKKRISMKNLLNHPWIMQDYNYPVEWQSKNPFIHLDDDCVTELSVHHRNNRQTMEDLISLWQYDHLTATYLLLLAKKARGKPVRLRLSSFSCG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.91
R work: 0.2861
R free: 0.3302
Average B factor: 107.7423
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: PEG 4000
Matthews coefficient: 2.4
Solvent content (%): 48.72
Ligand: 2-(benzyloxy)-4-(1H-pyrazol-4-yl)-N-(2,3,4,5-tetrahydro-1H-3-benzazepin-7-yl)benzamide (7LY)
Ligand formula: C27 H26 N4 O2
Ligand molecular weight: 438.521
Ligand SMILES: c1ccc(cc1)COc2cc(ccc2C(=O)Nc3ccc4c(c3)CCNCC4)c5c[nH]nc5
Ligand InChI: InChI=1S/C27H26N4O2/c32-27(31-24-8-6-20-10-12-28-13-11-22(20)14-24)25-9-7-21(23-16-29-30-17-23)15-26(25)33-18-19-4-2-1-3-5-19/h1-9,14-17,28H,10-13,18H2,(H,29,30)(H,31,32)
Release date: 2017-11-22
Structure of human PARP1 catalytic domain bound to a benzoimidazole inhibitor (PDB entry 5WS1)
Macromolecule: Poly [ADP-ribose] polymerase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.2.30
Sequence length: 352 residues
Sequence: HMKSKLPKPVQDLIKMIFDVESMKKAMVEYEIDLQKMPLGKLSKRQIQAAYSILSEVQQAVSQGSSDSQILDLSNRFYTLIPHDFGMKKPPLLNNADSVQAKAEMLDNLLDIEVAYSLLRGGSDDSSKDPIDVNYEKLKTDIKVVDRDSEEAEIIRKYVKNTHATTHNAYDLEVIDIFKIEREGECQRYKPFKQLHNRRLLWHGSRTTNFAGILSQGLRIAPPEAPVTGYMFGKGIYFADMVSKSANYCHTSQGDPIGLILLGEVALGNMYELKHASHISKLPKGKHSVKGLGKTTPDPSANISLDGVDVPLGTGISSGVNDTSLLYNEYIVYDIAQVNLKYLLKLKFNFKT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.23304
R free: 0.27332
Average B factor: 22.509
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 298
Crystal growth procedure: 2.5M AMMONIUM SULFATE, 100mM TRIS
Matthews coefficient: 2.3
Solvent content (%): 46.54
Ligand: 2-[(3R)-3-azanylpyrrolidin-1-yl]carbonyl-1H-benzimidazole-4-carboxamide (7U9)
Ligand formula: C13 H15 N5 O2
Ligand molecular weight: 273.291
Ligand SMILES: c1cc(c2c(c1)[nH]c(n2)C(=O)N3CCC(C3)N)C(=O)N
Ligand InChI: InChI=1S/C13H15N5O2/c14-7-4-5-18(6-7)13(20)12-16-9-3-1-2-8(11(15)19)10(9)17-12/h1-3,7H,4-6,14H2,(H2,15,19)(H,16,17)/t7-/m1/s1
Release date: 2017-01-25
X-ray structure of human PPARalpha ligand binding domain-fenofibric acid-SRC1 coactivator peptide co-crystals obtained by delipidation and co-crystallization (PDB entry 7BQ0)
Macromolecule: Peroxisome proliferator-activated receptor alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 273 residues
Sequence: GSHMTADLKSLAKRIYEAYLKNFNMNKVKARVILSGKASNNPPFVIHDMETLCMAEKTLVAKLVANGIQNKEAEVRIFHCCQCTSVETVTELTEFAKAIPGFANLDLNDQVTLLKYGVYEAIFAMLSSVMNKDGMLVAYGNGFITREFLKSLRKPFCDIMEPKFDFAMKFNALELDDSDISLFVAAIICCGDRPGLLNVGHIEKMQEGIVHVLRLHLQSNHPDDIFLFPKLLQKMADLRQLVTEHAQLVQIIKKTESDAALHPLLQEIYRDMY
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.771
R work: 0.1899
R free: 0.2173
Average B factor: 34.8344
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M Tris (pH 8.5), 25 %(w/v) PEG3350
Matthews coefficient: 2.83
Solvent content (%): 56.53
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: 2020-11-11