satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal Structure of Drosophila DHX36 helicase in complex with CTCTCCT (PDB entry 5N8U)
Macromolecule: CG9323, isoform A
Type: Protein, polypeptide(L)
Source organism: Drosophila melanogaster
EC number: 3.6.1.3
Sequence length: 944 residues
Sequence: MQRDRDSSGSNARKGNRPPGLRGKDIGLYYRNLARQQKKDRGENAESKEPQIRLGCNVSAPSGVLERVKELMEDYSRAPSRQNVDDKNVDAKFQQQFRHLLSVNFEEFVAETKERNADLDWVNPKLDERLQLELGQRQLEENAKKRLEARKKLPTMKYADDIIQAVRENQVILIVGSTGCGKTTQVPQILLDDAISRGCASSCRIICTQPRRISAIAIAEWVSYERCESLGNSVGYQIRLESRKARERASITYCTTGVLLQQLQSDPLMHNLSVLILDEIHERSVETDLLMGLLKVILPHRPDLKVILMSATVREQDFCDYFNNCPMFRIEGVMFPVKMLYLEDVLSKTNYEFQKFRDRRPKRDPPERRMKHEAMIEPYLRRIRNSYDSRVLDKLRLPESEGCEDIDFIADLVYYICENEPEGAILVFLPGYDKISQLYNILDKPKTSKGQRWRDHMAVFPLHSLMQSGEQQAVFRRPPAGQRKVIISTIIAETSVTIDDVVYVINSGRTKATNYDIETNIQSLDEVWVTKANTQQRRGRAGRVRPGICYNLFSRAREDRMDDIPTPEILRSKLESIILSLKLLHIDDPYRFLQTLINAPNPEAIKMGVELLKRIEALDQTGTLTPLGMHLAKLPIDPQMGKMILMSALFCCLDPITSAAAALSFKSPFYSPLGKESRVDEIKRRMARNMRSDHLMVHNTIIAYRDSRYSHAERDFCYKNFLSSMTLQQLERMKNQFSELLYNYKFLASSNCKDAASNKNSEKIPLLRAIIGAGLYPNMAHLRKSRQIKNRVRAIHTMATDDGRRVNFHPSSVNSGESGFDSAYFVYFQRQKSTDLFLLDSTMVFPMALIIFGDGVEAGVTQNTPYLCVAKTYYFKCNRETADVVIQLRSNLEKLLLKKALYPAPIEENGYEKQLIKAIELLLSLDERLGEDYISSDEIDDIVD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.62
R work: 0.1825
R free: 0.2495
Average B factor: 57.46
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 298
Crystal growth procedure: 0.1M MES monohydrate-imidazole
20mM sodium formate
20mM ammonium acetate
20mM sodium citrate tribasic hydrate
20mM sodium oxamate
20mM potassium sodium tartrate tetrahydrate
Matthews coefficient: 2.69
Solvent content (%): 54.3
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: 2018-03-14
PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of NUDT7 in complex with OX-65 (PDB entry 5QGQ)
Macromolecule: Peroxisomal coenzyme A diphosphatase NUDT7
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1
Sequence length: 196 residues
Sequence: SMLDDAKARLRKYDIGGKYSHLPYNKYSVLLPLVAKEGKLHLLFTVRSEKLRRAPGEVCFPGGKRDPTDMDDAATALREAQEEVGLRPHQVEVVCCLVPCLIDTDTLITPFVGLIDHNFQAQPNPAEVKDVFLVPLAYFLHPQVHDQHYVTRLGHRFINHIFEYTNPEDGVTYQIKGMTANLAVLVAFIILEKKPT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.95
R work: 0.2019
R free: 0.2269
Average B factor: 34.415
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M bis-tris pH 5.5 -- 0.1M ammonium acetate -- 5%(w/v) PEG10K
Matthews coefficient: 4.33
Solvent content (%): 71.59
Ligand: ACETATE ION (ACT)
Ligand formula: C2 H3 O2
Ligand molecular weight: 59.044
Ligand SMILES: CC(=O)[O-]
Ligand InChI: InChI=1S/C2H4O2/c1-2(3)4/h1H3,(H,3,4)/p-1
Release date: 2019-03-27
Structure of the unliganded form of the proprotein convertase furin. (PDB entry 5JXG)
Macromolecule: Furin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.75
Sequence length: 482 residues
Sequence: DVYQEPTDPKFPQQWYLSGVTQRDLNVKAAWAQGYTGHGIVVSILDDGIEKNHPDLAGNYDPGASFDVNDQDPDPQPRYTQMNDNRHGTRCAGEVAAVANNGVCGVGVAYNARIGGVRMLDGEVTDAVEARSLGLNPNHIHIYSASWGPEDDGKTVDGPARLAEEAFFRGVSQGRGGLGSIFVWASGNGGREHDSCNCDGYTNSIYTLSISSATQFGNVPWYSEACSSTLATTYSSGNQNEKQIVTTDLRQKCTESHTGTSASAPLAAGIIALTLEANKNLTWRDMQHLVVQTSKPAHLNANDWATNGVGRKVSHSYGYGLLDAGAMVALAQNWTTVAPQRKCIIDILTEPKDIGKRLEVRKTVTACLGEPNHITRLEHAQARLTLSYNRRGDLAIHLVSPMGTRSTLLAARPHDYSADGFNDWAFMTTHSWDEDPSGEWVLEIENTSEANNYGTLTKFTLVLYGTASGSLVPRGSHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.154
R free: 0.1733
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293.15
Crystal growth procedure: crystallization solution: 100 mM MES, 200 mM K/NaH2PO4, pH 5.5-6.0, 3-4 M NaCl, 3% DMSO; reservoir solution: 3-4 M NaCl
Matthews coefficient: 3.73
Solvent content (%): 67.05
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: 2016-10-05
Structure of Chlamydia trachomatis effector protein Cdu1 bound to ubiquitin (PDB entry 6FDK)
Macromolecule: Deubiquitinase and deneddylase Dub1
Type: Protein, polypeptide(L)
Source organism: Chlamydia trachomatis L2/434/Bu
EC number: 3.4.22
Sequence length: 266 residues
Sequence: MKHHHHHHSAGLEVLFQGPRRQTIEALVPAWDSDIIFKALCYFHTLYPGLIPLETFPPATIFNFKQKIISILEDKKAVLRGEPIKGPLPISCSKENYRRHLQRTTLLPVFMWYHPTPKTLSDTMQTMKQLAIKGSVGASHWLLVIVDIQARRLVYFDSLYNYVMPPENMKKELQSFAQQLDQVYPAYDSKKFSVKIAAKEVIQRGSGSSCGAWCCQFLHWYLKDPLTDALNDLPVDSVERHENLASFVQAAEAAVQDLPELSWPEA
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.16955
R free: 0.20333
Average B factor: 23.148
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293.15
Crystal growth procedure: 0.1 M MES pH 6.5, 12% PEG 20000
Matthews coefficient: 2.05
Solvent content (%): 39.91
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: 2018-08-15
APE1 exonuclease product complex (PDB entry 5WN1)
Macromolecule: DNA-(apurinic or apyrimidinic site) lyase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1
Sequence length: 276 residues
Sequence: ALYEDPPDQKTSPSGKPATLKICSWNVDGLRAWIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQELPGLSHQYWSAPSDKEGYSGVGLLSRQAPLKVSYGIGDEEHDQEGRVIVAEFDSFVLVTAYVPNAGRGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLRNPKGNKKNAGFTPQERQGFGELLQAVPLADSFRHLYPNTPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIRSKALGSDHCPITLYLAL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.2127
R free: 0.27
Average B factor: 47.8056
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5
Crystallization temperature (K): 291
Crystal growth procedure: 7% PEG20000, 100 mM sodium citrate, 15% glycerol, 5 mM calcium chloride
Matthews coefficient: 2.6
Solvent content (%): 52.78
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: 2018-02-28
Crystal Structure of Monobody Mb(SHP2PTP_13)/SHP2 PTP Domain Complex (PDB entry 7TVJ)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 11
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 304 residues
Sequence: GSAEIESRVRELSKLAETTDKVKQGFWEEFETLQQQECKLLYSRKEGQRQENKNKNRYKNILPFDHTRVVLHDGDPNEPVSDYINANIIMPEFETKCNNSKPKKSYIATQGCLQNTVNDFWRMVFQENSRVIVMTTKEVERGKSKCVKYWPDEYALKEYGVMRVRNVKESAAHDYTLRELKLSKVGQGNTERTVWQYHFRTWPDHGVPSDPGGVLDFLEEVHHKQESIMDAGPVVVHCSAGIGRTGTFIVIDILIDIIREKGVDCDIDVPKTIQMVRSQRSGMVQTEAQYRFIYMAVQHYIETL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.39
R work: 0.2291
R free: 0.2588
Average B factor: 34.15
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 5
Crystallization temperature (K): 292
Crystal growth procedure: 0.1 M sodium citrate tribasic dihydrate, 2% Tascimate, 16% PEG3350
Matthews coefficient: 2.26
Solvent content (%): 45.64
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: 2023-02-15
Crystal structure of the complex of DNase I/G-actin/PPP1R15A_582-621 (PDB entry 7NXV)
Macromolecule: Actin, alpha skeletal muscle, intermediate form
Type: Protein, polypeptide(L)
Source organism: Oryctolagus cuniculus
Sequence length: 375 residues
Sequence: DEDETTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREKMTQIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDLAGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEKSYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNVMSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWITKQEYDEAGPSIVHRKCF
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.55
R work: 0.2159
R free: 0.2478
Average B factor: 36.137
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 5
Crystallization temperature (K): 293
Crystal growth procedure: 10% PEG4000, 0.1M Acetate
Matthews coefficient: 2.87
Solvent content (%): 57.11
Ligand: ADENOSINE-5'-TRIPHOSPHATE (ATP)
Ligand formula: C10 H16 N5 O13 P3
Ligand molecular weight: 507.181
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N
Ligand InChI: InChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
Release date: 2021-09-29
Crystal Structure of human phosphodiesterase 10 in complex with 3-[2-(6,8-dichloro-5-methyl-[1,2,4]triazolo[1,5-a]pyridin-2-yl)ethyl]-1H-quinoxalin-2-one (PDB entry 5SIU)
Macromolecule: cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.17
Sequence length: 343 residues
Sequence: GSSICTSEEWQGLMQFTLPVRLCKEIELFHFDIGPFENMWPGIFVYMVHRSCGTSCFELEKLCRFIMSVKKNYRRVPYHNWKHAVTVAHCMYAILQNNHTLFTDLERKGLLIACLCHDLDHRGFSNSYLQKFDHPLAALYSTSTMEQHHFSQTVSILQLEGHNIFSTLSSSEYEQVLEIIRKAIIATDLALYFGNRKQLEEMYQTGSLNLNNQSHRDRVIGLMMTACDLCSVTKLWPVTKLTANDIYAEFWAEGDEMKKLGIQPIPMMDRDKKDEVPQGQLGFYNAVAIPCYTTLTQILPPTEPLLKACRDNLSQWEKVIRGEETATWISSPSVAQKAAASED
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.01
R work: 0.1697
R free: 0.2116
Average B factor: 38.195
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 295
Crystal growth procedure: 5-20 mg/mL protein in 25mM HEPES/NaOH pH7.5, 150mM NaCl, 50mM BME mixed 1:1 with reservoir 0.1M HEPES/NaOH pH7.5, 30% PEG550MME, 50mM MgCl2
Matthews coefficient: 2.62
Solvent content (%): 53.12
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: 2022-10-12
crystal structure of point mutated DUSP19 (C150A) (PDB entry 4D3P)
Macromolecule: DUAL SPECIFICITY PROTEIN PHOSPHATASE 19
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.16
Sequence length: 147 residues
Sequence: GSHMASQVGVIKPWLLLGSQDAAHDLDTLKKNKVTHILNVAYGVENAFLSDFTYKSISILDLPETNILSYFPECFEFIEEAKRKDGVVLVHANAGVSRAAAIVIGFLMNSEQTSFTSAFSLVKNARPSICPNSGFMEQLRTYQEGKE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.27
R work: 0.1551
R free: 0.17762
Average B factor: 8.807
Crystal growth procedure: 1.8M AMMONIUM SULFATE
Matthews coefficient: 2.27
Solvent content (%): 45.96
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: 2015-11-04
Crystal Structure of human phosphodiesterase 10 in complex with 3-(2-quinolin-4-ylpyrazol-3-yl)-1-[3-(trifluoromethoxy)phenyl]pyridazin-4-one (PDB entry 5SJF)
Macromolecule: cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.17
Sequence length: 343 residues
Sequence: GSSICTSEEWQGLMQFTLPVRLCKEIELFHFDIGPFENMWPGIFVYMVHRSCGTSCFELEKLCRFIMSVKKNYRRVPYHNWKHAVTVAHCMYAILQNNHTLFTDLERKGLLIACLCHDLDHRGFSNSYLQKFDHPLAALYSTSTMEQHHFSQTVSILQLEGHNIFSTLSSSEYEQVLEIIRKAIIATDLALYFGNRKQLEEMYQTGSLNLNNQSHRDRVIGLMMTACDLCSVTKLWPVTKLTANDIYAEFWAEGDEMKKLGIQPIPMMDRDKKDEVPQGQLGFYNAVAIPCYTTLTQILPPTEPLLKACRDNLSQWEKVIRGEETATWISSPSVAQKAAASED
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.05
R work: 0.1875
R free: 0.2274
Average B factor: 43.69
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 295
Crystal growth procedure: 5-20 mg/mL protein in 25mM HEPES/NaOH pH7.5, 150mM NaCl, 50mM BME mixed 1:1 with reservoir 0.1M HEPES/NaOH pH7.5, 30% PEG550MME, 50mM MgCl2
Matthews coefficient: 2.7
Solvent content (%): 54.48
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: 2022-10-12
Crystal structure of the ACVR1 (ALK2) kinase in complex with the compound Momelotinib (PDB entry 7NNS)
Macromolecule: Activin receptor type I
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.30
Sequence length: 301 residues
Sequence: SMQRTVARDITLLECVGKGRYGEVWRGSWQGENVAVKIFSSRDEKSWFRETELYNTVMLRHENILGFIASDMTSRHSSTQLWLITHYHEMGSLYDYLQLTTLDTVSCLRIVLSIASGLAHLHIEIFGTQGKPAIAHRDLKSKNILVKKNGQCCIADLGLAVMHSQSTNQLDVGNNPRVGTKRYMAPEVLDETIQVDCFDSYKRVDIWAFGLVLWEVARRMVSNGIVEDYKPPFYDVVPNDPSFEDMRKVVCVDQQRPNIPNRWFSDPTLTSLAKLMKECWYQNPSARLTALRIKKTLTKID
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.14
R work: 0.2284
R free: 0.2689
Average B factor: 28.5963
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 1.4M ammonium sulfate, 0.1M tris pH 7.5, 8% glycerol.
Matthews coefficient: 2.71
Solvent content (%): 54.63
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: 2021-04-07
Crystal Structure of panitumumab in complex with epidermal growth factor receptor domain 3 mutant S468R. (PDB entry 5SX5)
Macromolecule: Panitumumab Fab Light Chain
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 214 residues
Sequence: DIQMTQSPSSLSASVGDRVTITCQASQDISNYLNWYQQKPGKAPKLLIYDASNLETGVPSRFSGSGSGTDFTFTISSLQPEDIATYFCQHFDHLPLAFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.2257
R free: 0.2498
Average B factor: 55.5934
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 2.0 M AmSO4, 100 mM MES 6.5  and 5% peg 400
Matthews coefficient: 3.07
Solvent content (%): 59.94
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: 2016-10-05
Inhibitor Complex with Thrombin Activatable Fibrinolysis inhibitor (TAFIa) (PDB entry 7NEE)
Macromolecule: Carboxypeptidase B2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.17.20
Sequence length: 400 residues
Sequence: QSGQVLAALPRTSRQVQVLQNLTTTYEIVLWQPVTADLIVKKKQVHFFVNASDVDNVKAHLNVSGIPCSVLLADVEDLIQQQISNDTVSPRASASYYEQYHSLNEIYSWIEFITERHPDMLTKIHIGSSFEKYPLYVLKVSGKEQAAKNAIWIDCGIHAREWISPAFCLWFIGHITQFYGIIGQYTNLLRLVDFYVMPVVNVDGYDYSWKKNRMWRKNRSFYANNHCIGTDLNRNFASKHWCEEGASSSSCSETYCGLYPESEPEVKAVASFLRRNINQIKAYISMHSYSQHIVFPYSYTRSKCKDHEELSLVASEAVRAIEKISKNIRYTYGQGSETLYLAPGGGDDWIYDLGIKYSFTIELRDTGTYGFLLPERYIKPTCREAFAAVSKIAWHVIRNV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.55
R work: 0.2543
R free: 0.3156
Average B factor: 39.852
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 23% PEG 8000, 200mM Ammonium Citrate, 100 mM MES
Matthews coefficient: 2.62
Solvent content (%): 53.09
Ligand: (1R,3S)-3-(4-ammoniobutyl)-1-benzyl-1,4-azaphosphinan-1-ium-3-carboxylate 4,4-dioxide (U9B)
Ligand formula: C16 H27 N2 O4 P
Ligand molecular weight: 342.37
Ligand SMILES: c1ccc(cc1)C[NH+]2CCP(=O)(C(C2)(CCCC[NH3+])C(=O)O)O
Ligand InChI: InChI=1S/C16H25N2O4P/c17-9-5-4-8-16(15(19)20)13-18(10-11-23(16,21)22)12-14-6-2-1-3-7-14/h1-3,6-7H,4-5,8-13,17H2,(H,19,20)(H,21,22)/p+2/t16-/m0/s1
Release date: 2021-04-07
Crystal structure of GTA + A trisaccharide (mercury derivative) (PDB entry 5TJL)
Macromolecule: Histo-blood group ABO system transferase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.1.40
Sequence length: 297 residues
Sequence: AIGEFMVSLPRMVYPQPKVLTPCRKDVLVVTPWLAPIVWEGTFNIDILNEQFRLQNTTIGLTVFAIKKYVAFLKLFLETAEKHFMVGHRVHYYVFTDQPAAVPRVTLGTGRQLSVLEVRAYKRWQDVSMRRMEMISDFCERRFLSEVDYLVCVDVDMEFRDHVGVEILTPLFGTLHPGFYGSSREAFTYERRPQSQAYIPKDEGDFYYLGGFFGGSVQEVQRLTRACHQAMMVDQANGIEAVWHDESHLNKYLLRHKPTKVLSPEYLWDQQLLGWPAVLRKLRFTAVPKNHQAVRNP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.89
R work: 0.1879
R free: 0.2236
Average B factor: 31.273
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 277
Crystal growth procedure: The first crystals of GTA/GTB were grown as mercury derivatives (Patenaude, S.I., et al. 2002): 10 ul drops with 6-8 mg/ml protein, 70 mM N-(2-acetamido)-2-iminodiacetic acid (ADA) pH 7.5, 50 mM, sodium acetate pH 4.6, 40 mM NaCl, 5-8 mM MnCl2, 2.5% (v/v) 2-methyl-2,4-pentanediol (MPD), 5%(v/v) glycerol, 2%(w/v) PEG 4000, and 0.3-0.5 mM 3-chloromercuri-2-methoxypropylurea suspended over 1 ml of a resevoir solution: 50 mM ADA pH 7.5, 10 mM MnCl2, 100 mM ammonium sulfate, 5%(v/v) MPD, 10%(v/v) glycerol, and 8-10%(w/v) PEG 4000. Crystals were washed with artificial mother liquor ML-1 consisting of 10% polyethylene glycol (PEG) 4000, 30 mM N-(2-acetamido)-2-iminodiacetic acid (ADA) buffer pH 7.5, 30 mM sodium acetate buffer pH 4.6, 100 mM ammonium sulfate, 10 mM MnCl2 and 30% glycerol as the cryoprotectant. Crystals of GTA/GTB in complex with the A and B trisaccharides were obtained by soaking them in mother liquor ML-1 with 30% glycerol and 45-50 mM substrates for 2-5 days at 18 degrees Celsius
Matthews coefficient: 2.26
Solvent content (%): 45.66
Ligand: MERCURY (II) ION (HG)
Ligand formula: Hg
Ligand molecular weight: 200.59
Ligand SMILES: [Hg+2]
Ligand InChI: InChI=1S/Hg/q+2
Release date: 2017-06-14
Pyk2-FAT complexed with Leupaxin LD motif LD1 (PDB entry 4XEF)
Macromolecule: Protein-tyrosine kinase 2-beta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 139 residues
Sequence: GSHMANLDRTDDLVYLNVMELVRAVLELKNELSQLPPEGYVVVVKNVGLTLRKLIGSVDDLLPSLPSSSRTEIEGTQKLLNKDLAELINKMRLAQQNAVTSLSEEAKRQMLTASHTLAVDAKNLLDAVDQAKVLANLAH
Oligomeric state: Hetero 3-mer
Stoichiometry: A2, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.224
R free: 0.266
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 291
Crystal growth procedure: 400 nl drop contained 200 nl protein/LD1 peptide mixture (20 mM MES, pH 6.2, 1 mM protein, and 2 mM peptide) and 200 nl well solution (100 mM Tris, pH 8.5, 0.2 M MgCl2, and 30% PEG 4000).
Matthews coefficient: 2.23
Solvent content (%): 44.83
Release date: 2015-12-23
Nido-carborane butyl-sulfonamide in complex with CA IX mimic (PDB entry 6Z04)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 260 residues
Sequence: MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHSFQVTFDDSQDKAVLKGGPLDGTYRLLQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDVGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTEGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLAECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.05
R work: 0.1408
R free: 0.1578
Average B factor: 15.626
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 50 mM Tris pH=7.8
1.6 M Natrium Citrate
Matthews coefficient: 2.1
Solvent content (%): 41.4
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: 2020-10-28
Crystal Structure of Cathepsin-G and Neutrophil Elastase Inhibited by S. aureus EapH2 at pH 8.5 (PDB entry 8G26)
Macromolecule: Cathepsin-G
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 223 residues
Sequence: IIGGRESRPHSRPYMAYLQIQSPAGQSRCGGFLVREDFVLTAAHCWGSNINVTLGAHNIQRRENTQQHITARRAIRHPQYNQRTIQNDIMLLQLSRRVRRNRNVNPVALPRAQEGLRPGTLCTVAGWGRVSMRRGTDTLREVQLRVQRDRQCLRIFGSYDPRRQICVGDRRERKAAFKGDSGGPLLCNNVAHGIVSYGKSSGVPPEVFTRVSSFLPWIRTTMR
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.85
R work: 0.2028
R free: 0.2376
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M Tris, 0.2 M magnesium chloride, 25% PEG3350
Matthews coefficient: 2.22
Solvent content (%): 44.64
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: 2023-04-26
Crystal structure of UBR box of UBR4 apo (PDB entry 8J9Q)
Macromolecule: E3 ubiquitin-protein ligase UBR4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.27
Sequence length: 73 residues
Sequence: GHMKLCTFTITQKEFMNQHWYHCHTCKMVDGVGVCTVCAKVCHKDHEISYAKYGSFFCDCGAKEDGSCLALVK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.18
R work: 0.2192
R free: 0.2688
Average B factor: 49.78
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 291.15
Crystal growth procedure: 0.1 M DL-malic acid (pH7.0) and 18% (w/v) polyethylene glycol 3350 (PEG3350)
Matthews coefficient: 2.92
Solvent content (%): 57.89
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: 2023-12-06
Crystal Structure of human phosphodiesterase 10 in complex with 3-N-[2-(3-chlorophenyl)-1H-benzimidazol-5-yl]-2-methylpyrazole-3,4-dicarboxamide (PDB entry 5SG4)
Macromolecule: cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.17
Sequence length: 343 residues
Sequence: GSSICTSEEWQGLMQFTLPVRLCKEIELFHFDIGPFENMWPGIFVYMVHRSCGTSCFELEKLCRFIMSVKKNYRRVPYHNWKHAVTVAHCMYAILQNNHTLFTDLERKGLLIACLCHDLDHRGFSNSYLQKFDHPLAALYSTSTMEQHHFSQTVSILQLEGHNIFSTLSSSEYEQVLEIIRKAIIATDLALYFGNRKQLEEMYQTGSLNLNNQSHRDRVIGLMMTACDLCSVTKLWPVTKLTANDIYAEFWAEGDEMKKLGIQPIPMMDRDKKDEVPQGQLGFYNAVAIPCYTTLTQILPPTEPLLKACRDNLSQWEKVIRGEETATWISSPSVAQKAAASED
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.1697
R free: 0.222
Average B factor: 42.609
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 295
Crystal growth procedure: 5-20 mg/mL protein in 25mM HEPES/NaOH pH7.5, 150mM NaCl, 50mM BME mixed 1:1 with reservoir 0.1M HEPES/NaOH pH7.5, 30% PEG550MME, 50mM MgCl2
Matthews coefficient: 3
Solvent content (%): 58.95
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: 2022-10-12