satarupa22/MacromolecularLigandDB huggingface dataset:
CRYSTAL STRUCTURE OF RHO-ASSOCIATED PROTEIN KINASE 2 (ROCK2) IN COMPLEX WITH 4-(4-(2-(2,3-DIHYDRO-1H- INDOL-1-YL)-2-OXOETHYL)PHENYL)-1(2H)-PHTHALAZINONE (PDB entry 8GDS)
Macromolecule: Rho-associated protein kinase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 396 residues
Sequence: AGASRQRKLEALIRDPRSPINVESLLDGLNSLVLDLDFPALRKNKNIDNFLNRYEKIVKKIRGLQMKAEDYDVVKVIGRGAFGEVQLVRHKASQKVYAMKLLSKFEMIKRSDSAFFWEERDIMAFANSPWVVQLFYAFQDDRYLYMVMEYMPGGDLVNLMSNYDVPEKWAKFYTAEVVLALDAIHSMGLIHRDVKPDNMLLDKHGHLKLADFGTCMKMDETGMVHCDTAVGTPDYISPEVLKSQGGDGFYGRECDWWSVGVFLYEMLVGDTPFYADSLVGTYSKIMDHKNSLCFPEDAEISKHAKNLICAFLTDREVRLGRNGVEEIRQHPFFKNDQWHWDNIRETAAPVVPELSSDIDSSNFDDIEDDKGDVETFPIPKAFVGNQLPFIGFTYYR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.71
R work: 0.2175
R free: 0.2477
Average B factor: 52.85
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Matthews coefficient: 3.79
Solvent content (%): 67.52
Ligand: 4-{4-[2-(2,3-dihydro-1H-indol-1-yl)-2-oxoethyl]phenyl}phthalazin-1(2H)-one (Z8O)
Ligand formula: C24 H19 N3 O2
Ligand molecular weight: 381.427
Ligand SMILES: c1ccc2c(c1)CCN2C(=O)Cc3ccc(cc3)C4=NNC(=O)c5c4cccc5
Ligand InChI: InChI=1S/C24H19N3O2/c28-22(27-14-13-17-5-1-4-8-21(17)27)15-16-9-11-18(12-10-16)23-19-6-2-3-7-20(19)24(29)26-25-23/h1-12H,13-15H2,(H,26,29)
Release date: 2023-05-10
Crystal structure of human glutaminyl cyclase variant Y115E-Y117E in complex with SEN177 (PDB entry 6GBX)
Macromolecule: Glutaminyl-peptide cyclotransferase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.5
Sequence length: 329 residues
Sequence: ASAWPEEKNYHQPAILNSSALRQIAEGTSISEMWQNDLQPLLIERYPGSPGSYAARQHIMQRIQRLQADWVLEIDTFLSQTPEGERSFSNIISTLNPTAKRHLVLACHYDSKYFSHWNNRVFVGATDSAVPCAMMLELARALDKKLLSLKTVSDSKPDLSLQLIFFDGEEAFLHWSPQDSLYGSRHLAAKMASTPHPPGARGTSQLHGMDLLVLLDLIGAPNPTFPNFFPNSARWFERLQAIEHELHELGLLKDHSLEGRYFQNYSYGGVIQDDHIPFLRRGVPVLHLIPSPFPEVWHTMDDNEENLDESTIDNLNKILQVFVLEYLHL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.72
R work: 0.15819
R free: 0.18307
Average B factor: 15.516
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 277.15
Crystal growth procedure: 0.1 M MES, 0.4 M ammonium sulfate, 0.07 M sodium chloride
Matthews coefficient: 2.44
Solvent content (%): 49.6
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: 2018-09-19
Crystal structure of dipeptidyl peptidase IV in complex with SYR-472 (PDB entry 5KBY)
Macromolecule: Dipeptidyl peptidase 4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.14.5
Sequence length: 740 residues
Sequence: ADPGGSHHHHHHSRKTYTLTDYLKNTYRLKLYSLRWISDHEYLYKQENNILVFNAEYGNSSVFLENSTFDEFGHSINDYSISPDGQFILLEYNYVKQWRHSYTASYDIYDLNKRQLITEERIPNNTQWVTWSPVGHKLAYVWNNDIYVKIEPNLPSYRITWTGKEDIIYNGITDWVYEEEVFSAYSALWWSPNGTFLAYAQFNDTEVPLIEYSFYSDESLQYPKTVRVPYPKAGAVNPTVKFFVVNTDSLSSVTNATSIQITAPASMLIGDHYLCDVTWATQERISLQWLRRIQNYSVMDICDYDESSGRWNCLVARQHIEMSTTGWVGRFRPSEPHFTLDGNSFYKIISNEEGYRHICYFQIDKKDCTFITKGTWEVIGIEALTSDYLYYISNEYKGMPGGRNLYKIQLSDYTKVTCLSCELNPERCQYYSVSFSKEAKYYQLRCSGPGLPLYTLHSSVNDKGLRVLEDNSALDKMLQNVQMPSKKLDFIILNETKFWYQMILPPHFDKSKKYPLLLDVYAGPCSQKADTVFRLNWATYLASTENIIVASFDGRGSGYQGDKIMHAINRRLGTFEVEDQIEAARQFSKMGFVDNKRIAIWGWSYGGYVTSMVLGSGSGVFKCGIAVAPVSRWEYYDSVYTERYMGLPTPEDNLDHYRNSTVMSRAENFKQVEYLLIHGTADDNVHFQQSAQISKALVDVGVDFQAMWYTDEDHGIASSTAHQHIYTHMSHFIKQCFSLP
Oligomeric state: Homo 2-mer
Stoichiometry: A2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.24
R work: 0.1743
R free: 0.215
Average B factor: 50.867
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 22.2% PEG MME 2000, 0.1M Bicine pH 8.5
Matthews coefficient: 2.85
Solvent content (%): 56.83
Ligand: 2-[[6-[(3~{R})-3-azanylpiperidin-1-yl]-3-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]methyl]-4-fluoranyl-benzenecarboni
trile (6RL)
Ligand formula: C18 H20 F N5 O2
Ligand molecular weight: 357.382
Ligand SMILES: CN1C(=O)C=C(N(C1=O)Cc2cc(ccc2C#N)F)N3CCCC(C3)N
Ligand InChI: InChI=1S/C18H20FN5O2/c1-22-17(25)8-16(23-6-2-3-15(21)11-23)24(18(22)26)10-13-7-14(19)5-4-12(13)9-20/h4-5,7-8,15H,2-3,6,10-11,21H2,1H3/t15-/m1/s1
Release date: 2016-07-13
Identification of a New Zinc Binding Chemotype by Fragment Screening (PDB entry 5TYA)
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): 1.5
R work: 0.10597
R free: 0.16486
Average B factor: 14.646
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.3
Crystallization temperature (K): 281
Crystal growth procedure: the reservoir condition consisted of 2.9 M ammonium sulfate with 0.1 M Tris buffer at pH 8.3; concentrated CA II at ~10 mg mL-1 was set up with seeding; dry compound was added to crystals several days before harvesting and data collection
Matthews coefficient: 2.09
Solvent content (%): 41.29
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: 2017-08-30
Crystal structure of human exonuclease 1 Exo1 (R92A) in complex with 5' flap DNA (uf4) (PDB entry 7MXX)
Macromolecule: Exonuclease 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1
Sequence length: 352 residues
Sequence: MGIQGLLQFIKEASEPIHVRKYKGQVVAVDTYCWLHKGAIACAEKLAKGEPTDRYVGFCMKFVNMLLSHGIKPILVFDGCTLPSKKEVERSARERRQANLLKGKQLLREGKVSEARECFTRSINITHAMAHKVIKAARSQGVDCLVAPYEADAQLAYLNKAGIVQAIITEDSDLLAFGCKKVILKMDQFGNGLEIDQARLGMCRQLGDVFTEEKFRYMCILSGCDYLSSLRGIGLAKACKVLRLANNPDIVKVIKKIGHYLKMNITVPEDYINGFIRANNTFLYQLVFDPIKRKLIPLNAYEDDVDPETLSYAGQYVDDSIALQIALGNKDINTFEQIDDYNPDTAMPAHSR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.85
R work: 0.2577
R free: 0.2976
Average B factor: 102.2851
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 290
Crystal growth procedure: 100 mM sodium acetate, pH 7.0; 10 mM KCl; 2mM CaCl2; 20 mM MnCl2; 2-4% PEG 4000
Matthews coefficient: 2.39
Solvent content (%): 48.52
Ligand: MANGANESE (II) ION (MN)
Ligand formula: Mn
Ligand molecular weight: 54.938
Ligand SMILES: [Mn+2]
Ligand InChI: InChI=1S/Mn/q+2
Release date: 2023-05-10
Human DJ-1 complexed with Na-K-tartrate (PDB entry 5IP5)
Macromolecule: Protein deglycase DJ-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.2
Sequence length: 189 residues
Sequence: MASKRALVILAKGAEEMETVIPVDVMRRAGIKVTVAGLAGKDPVQCSRDVVICPDASLEDAKKEGPYDVVVLPGGNLGAQNLSESAAVKEILKEQENRKGLIAAICAGPTALLAHEIGFGSKVTTHPLAKDKMMNGGHYTYSENRVEKDGLILTSRGPGTSFEFALAIVEALNGKEVAAQVKAPLVLKD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.66
R work: 0.14199
R free: 0.16391
Average B factor: 13.826
Crystallization method: MICROBATCH
Crystallization pH: 6.5
Crystallization temperature (K): 295
Crystal growth procedure: 1.5 M sodium potassium tartrate, 3.5 M ammonium sulfate, 0.1 M Na-Cacodylate
Matthews coefficient: 3.07
Solvent content (%): 59.99
Ligand: L(+)-TARTARIC ACID (TLA)
Ligand formula: C4 H6 O6
Ligand molecular weight: 150.087
Ligand SMILES: C(C(C(=O)O)O)(C(=O)O)O
Ligand InChI: InChI=1S/C4H6O6/c5-1(3(7)8)2(6)4(9)10/h1-2,5-6H,(H,7,8)(H,9,10)/t1-,2-/m1/s1
Release date: 2017-03-15
Scaffold-ligand complex with ligand unmodelled. (PDB entry 6YBM)
Macromolecule: Peptidyl-prolyl cis-trans isomerase F, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 165 residues
Sequence: MGNPLVYLDVDANGKPLGRVVLELKADVVPKTAENFRALCTGEKGFGYKGSTFHRVIPSFMCQAGDFTNHNGTGGKSIYGSRFPDENFTLKHVGPGVLSMANAGPNTNGSQFFICTIKTDWLDGKHVVFGHVIEGMDVVKKIESFGSKSGRTSKKIVITDCGQLS
Oligomeric state: Homo 3-mer
Stoichiometry: A3
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.41
R work: 0.1779
R free: 0.2112
Average B factor: 24.4
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 0.2 M Ammonium acetate, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 30% v/v (+/-)-2-Methyl-2,4-pentanediol
Matthews coefficient: 2.92
Solvent content (%): 57.93
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: 2020-04-15
Crystal structure of human tRNA-dihydrouridine (20) synthase dsRBD F359A mutant (PDB entry 6EI8)
Macromolecule: tRNA-dihydrouridine(20) synthase [NAD(P)+]-like
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.3.1
Sequence length: 120 residues
Sequence: MTSEQTGEPAEDTSGVIKMAVKADRRAYPAQITPKMCLLEWCRREKLAQPVYETVQRPLDRLFSSIVTVAEQKYQSTLWDKSKKLAEQAAAIVCLRSQGLPEGRLGEESPSLHKHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.25
R work: 0.259
R free: 0.286
Average B factor: 52.3
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 292
Crystal growth procedure: 2M ammonium sulfate
50 mM sodium cacodylate
15 mM magnesium acetate
Matthews coefficient: 3.9
Solvent content (%): 68.45
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: 2018-10-10
Crystal structure of TRIM7 bound to 2C (PDB entry 7Y3A)
Macromolecule: E3 ubiquitin-protein ligase TRIM7,E3 ubiquitin-protein ligase TRIM7,E3 ubiquitin-protein ligase TRIM7,TRIM7-2C
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.27
Sequence length: 193 residues
Sequence: KEEKVTLTLDPDTANPRLILSLDLKGVRLGERAQDLPNHPCRFDTNTRVLASCGFSSGRHHWEVEVGSKDGWAFGVARESVRRKGLTPFTPEEGVWALQLNGGQYWAVTSPERSPLSCGHLSRVRVALDLEVGAVSFYAVEDMRHLYTFRVNFQERVFPLFSVCSTGTYLRIWPGGSGGSGGSGGATLEALFQ
Oligomeric state: Homo 2-mer
Stoichiometry: A2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.1484
R free: 0.1751
Average B factor: 14.6624
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M Sodium formate pH 7.0 20%3350 0.2M NaCl
Matthews coefficient: 2.48
Solvent content (%): 50.31
Release date: 2022-08-03
Crystal structure of the human METTL3-METTL14 complex with compound UOZ083 (PDB entry 7OEI)
Macromolecule: N6-adenosine-methyltransferase catalytic subunit
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.348
Sequence length: 246 residues
Sequence: MGHHHHHHSSGRENLYFQGALTQSVGGDSSADRLFPPQWICCDIRYLDVSILGKFAVVMADPPWDIHMELPYGTLTDDEMRRLNIPVLQDDGFLFLWVTGRAMELGRECLNLWGYERVDEIIWVKTNQLQRIIRTGRTGHWLNHGKEHCLVGVKGNPQGFNQGLDCDVIVAEVRSTSHKPDEIYGMIERLSPGTRKIELFGRPHNVQPNWITLGNQLDGIHLLDPDVVARFKQRYPDGIISKPKNL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.48
R work: 0.1986
R free: 0.254
Average B factor: 55.8
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 295
Crystal growth procedure: 20% PEG 3350, 400mM Mg acetate
Matthews coefficient: 2.15
Solvent content (%): 42.76
Ligand: (3~{R})-3-[[5-[(4,4-dimethylpiperidin-1-yl)methyl]-1~{H}-benzimidazol-2-yl]methyl]-1-[6-[(phenylmethyl)amino]pyrimidin-4-yl]piperidin-3-ol (V9W)
Ligand formula: C32 H41 N7 O
Ligand molecular weight: 539.714
Ligand SMILES: CC1(CCN(CC1)Cc2ccc3c(c2)nc([nH]3)CC4(CCCN(C4)c5cc(ncn5)NCc6ccccc6)O)C
Ligand InChI: InChI=1S/C32H41N7O/c1-31(2)12-15-38(16-13-31)21-25-9-10-26-27(17-25)37-29(36-26)19-32(40)11-6-14-39(22-32)30-18-28(34-23-35-30)33-20-24-7-4-3-5-8-24/h3-5,7-10,17-18,23,40H,6,11-16,19-22H2,1-2H3,(H,36,37)(H,33,34,35)/t32-/m1/s1
Release date: 2021-10-20
Crystal structure of USP7/HAUSP in complex with ICP0 (PDB entry 5C56)
Macromolecule: Ubiquitin E3 ligase ICP0
Type: Protein, polypeptide(L)
Source organism: Human alphaherpesvirus 1
Sequence length: 21 residues
Sequence: SGPRGPRKCARKTRHAETSGA
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.685
R work: 0.2155
R free: 0.263
Average B factor: 76.2301
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 20% PEG3350, 0.2M Sodium Bromide
Matthews coefficient: 3.79
Solvent content (%): 67.52
Release date: 2015-07-08
CO2 release in human carbonic anhydrase II crystals: reveal histidine 64 and solvent dynamics (PDB entry 5YUI)
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): 1.2
R work: 0.10467
R free: 0.13395
Average B factor: 13.961
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 1.3M sodium citrate, 100mM TrisHCl pH 7.8
Matthews coefficient: 2.09
Solvent content (%): 41.2
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: 2018-08-01
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with XST00000847b (PDB entry 7FQV)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 321 residues
Sequence: MEMEKEFEQIDKSGSWAAIYQDIRHEASDFPSRVAKLPKNKNRNRYRDVSPFDHSRIKLHQEDNDYINASLIKMEEAQRSYILTQGPLPNTVGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQKEEKEMIFEDTNLKLTLISEDIKSYYTVRQLELENLTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRESGSLSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKDPSSVDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFIMGDSSVQDQWKELSHEDLEPPPEHIPPPPRPPKRILEPHN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.04
R work: 0.1873
R free: 0.2227
Average B factor: 41.585
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M HEPES, 0.3 M magnesium acetate, 13.5% PEG 8000, 2% ethanol, and 1 mM BME
Matthews coefficient: 3.31
Solvent content (%): 62.79
Ligand: N,N-dimethylpyridin-4-amine (JGD)
Ligand formula: C7 H10 N2
Ligand molecular weight: 122.168
Ligand SMILES: CN(C)c1ccncc1
Ligand InChI: InChI=1S/C7H10N2/c1-9(2)7-3-5-8-6-4-7/h3-6H,1-2H3
Release date: 2022-11-23
TRK-A IN COMPLEX WITH LIGAND 1 (PDB entry 6NPT)
Macromolecule: High affinity nerve growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 305 residues
Sequence: IENPQYFSDACVHHIKRRDIVLKWELGEGAFGKVFLAECHNLLPEQDKMLVAVKALKEASESARQDFQREAELLTMLQHQHIVRFFGVCTEGRPLLMVFEYMRHGDLNRFLRSHGPDAKLLAGGEDVAPGPLGLGQLLAVASQVAAGMVYLAGLHFVHRDLATRNCLVGQGLVVKIGDFGMSRDIYSTDYYRVGGRTMLPIRWMPPESILYRKFTTESDVWSFGVVLWEIFTYGKQPWYQLSNTEAIDCITQGRELERPRACPPEVYAIMRGCWQREPQQRHSIKDVHARLQALAQAPPVYLDVL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.19
R work: 0.22334
R free: 0.27646
Average B factor: 52.878
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277.15
Crystal growth procedure: The protein at a concentration of 10 mg/ml was mixed with 2mM of the ligand (diluted from 100 mM DMSO stock solution) for 1 hour on ice and crystallized at 4 deg C (hanging drop) from:
0.10 M KH2PO4/ 0.10 M NaH2PO4/ 0.10 M MES/NaOH pH 6.00 and 1.90 M NaCl (cryo: 25% glycerol in reservoir), or
18.00 % (w/v) PEG 3350, 0.20 M CaCl2, 0.10 M, MES pH=6.50 (cryo: direct).
Matthews coefficient: 2.57
Solvent content (%): 52.25
Ligand: 4-tert-butyl-N-(1,3-diphenyl-1H-pyrazol-5-yl)benzamide (KWY)
Ligand formula: C26 H25 N3 O
Ligand molecular weight: 395.496
Ligand SMILES: CC(C)(C)c1ccc(cc1)C(=O)Nc2cc(nn2c3ccccc3)c4ccccc4
Ligand InChI: InChI=1S/C26H25N3O/c1-26(2,3)21-16-14-20(15-17-21)25(30)27-24-18-23(19-10-6-4-7-11-19)28-29(24)22-12-8-5-9-13-22/h4-18H,1-3H3,(H,27,30)
Release date: 2019-05-22
Ca2+-Calmodulin in complex with human muscle form creatine kinase peptide in extended 1:2 binding mode (PDB entry 7BF2)
Macromolecule: Calmodulin-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 149 residues
Sequence: MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK
Oligomeric state: Hetero 3-mer
Stoichiometry: A2, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.43
R work: 0.2006
R free: 0.2281
Average B factor: 35.196
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 4.5
Crystallization temperature (K): 293
Crystal growth procedure: 25% PEG 1500, 0.1 M SPG buffer pH 4-5. 
CaM-CKBpeptide ratios of 1:4
Matthews coefficient: 1.77
Solvent content (%): 30.53
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: 2021-07-21
Crystal structure of CLK1 in complex with inhibitor 16 (PDB entry 6FT9)
Macromolecule: Dual specificity protein kinase CLK1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 339 residues
Sequence: SMHLICQSGDVLSARYEIVDTLGEGAFGKVVECIDHKAGGRHVAVKIVKNVDRYCEAARSEIQVLEHLNTTDPNSTFRCVQMLEWFEHHGHICIVFELLGLSTYDFIKENGFLPFRLDHIRKMAYQICKSVNFLHSNKLTHTDLKPENILFVQSDYTEAYNPKIKRDERTLINPDIKVVDFGSATYDDEHHSTLVSTRHYRAPEVILALGWSQPCDVWSIGCILIEYYLGFTVFPTHDSKEHLAMMERILGPLPKHMIQKTRKRKYFHHDRLDWDEHSSAGRYVSRACKPLKEFMLSQDVEHERLFDLIQKMLEYDPAKRITLREALKHPFFDLLKKSI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.87
R work: 0.16635
R free: 0.20167
Average B factor: 42.145
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277.15
Crystal growth procedure: 20% 1,2-propanediol, 10% glycerol, 0.1 M sodium/potassium phosphate
Matthews coefficient: 2.49
Solvent content (%): 50.63
Ligand: 2-bromanyl-3-phenyl-1~{H}-pyrrolo[3,4-g]indol-8-one (E6W)
Ligand formula: C16 H9 Br N2 O
Ligand molecular weight: 325.159
Ligand SMILES: c1ccc(cc1)c2c3ccc4c(c3[nH]c2Br)C(=O)N=C4
Ligand InChI: InChI=1S/C16H9BrN2O/c17-15-12(9-4-2-1-3-5-9)11-7-6-10-8-18-16(20)13(10)14(11)19-15/h1-8,19H
Release date: 2018-05-16
Crystal structure of the human CHIP-TPR domain in complex with a 6mer acetylated tau peptide (PDB entry 8GCK)
Macromolecule: E3 ubiquitin-protein ligase CHIP
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.27
Sequence length: 128 residues
Sequence: KSPSAQELKEQGNRLFVGRKYPEAAACYGRAITRNPLVAVYYTNRALCYLKMQQHEQALADCRRALELDGQSVKAHFFLGQCQLEMESYDEAIANLQRAYSLAKEQRLNFGDDIPSALRIAKKKRWNS
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.36823537069
R work: 0.192428531184
R free: 0.209939305154
Average B factor: 21.5993112746
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 0.1 M CaCl2, 0.1 M HEPES pH 7.4, 25% PEG 3350
Matthews coefficient: 2
Solvent content (%): 34.46
Release date: 2024-03-06
Crystal structure of human 14-3-3 protein beta in complex with CFTR peptide pS753pS768 and PPI stabilizer CY007424 (PDB entry 7QI1)
Macromolecule: 14-3-3 protein theta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 237 residues
Sequence: GAMGSMTMDKSELVQKAKLAEQAERYDDMAAAMKAVTEQGHELSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTERNEKKQQMGKEYREKIEAELQDICNDVLELLDKYLIPNATQPESKVFYLKMKGDYFRYLSEVASGDNKQTTVSNSQQAYQEAFEISKKEMQPTHPIRLGLALNFSVFYYEILNSPEKACSLAKTAFDEAIAELDTLNEESYKDSTLIMQLLRDNLTLWTS
Oligomeric state: Hetero 6-mer
Stoichiometry: A4, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.76
R work: 0.1952
R free: 0.2411
Average B factor: 35.9
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: Qiagen Cryos Suite #44 (0.09 M HEPES sodium salt pH7.5, 1.26M tri-sodium citrate, 10% (v/v) glycerol) with an extra 2% (v/v) of glycerol.
Matthews coefficient: 2.26
Solvent content (%): 45.67
Ligand: ARGININE (ARG)
Ligand formula: C6 H15 N4 O2
Ligand molecular weight: 175.209
Ligand SMILES: C(CC(C(=O)O)N)CNC(=[NH2+])N
Ligand InChI: InChI=1S/C6H14N4O2/c7-4(5(11)12)2-1-3-10-6(8)9/h4H,1-3,7H2,(H,11,12)(H4,8,9,10)/p+1/t4-/m0/s1
Release date: 2022-05-25
Human Argonaute-2 bound to a guide RNA with a nucleobase modification at position 1 (PDB entry 5KI6)
Macromolecule: Protein argonaute-2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.26
Sequence length: 859 residues
Sequence: MYSGAGPALAPPAPPPPIQGYAFKPPPRPDFGTSGRTIKLQANFFEMDIPKIDIYHYELDIKPEKCPRRVNREIVEHMVQHFKTQIFGDRKPVFDGRKNLYTAMPLPIGRDKVELEVTLPGEGKDRIFKVSIKWVSCVSLQALHDALSGRLPSVPFETIQALDVVMRHLPSMRYTPVGRSFFTASEGCSNPLGGGREVWFGFHQSVRPSLWKMMLNIDVSATAFYKAQPVIEFVCEVLDFKSIEEQQKPLTDSQRVKFTKEIKGLKVEITHCGQMKRKYRVCNVTRRPASHQTFPLQQESGQTVECTVAQYFKDRHKLVLRYPHLPCLQVGQEQKHTYLPLEVCNIVAGQRCIKKLTDNQTSTMIRATARSAPDRQEEISKLMRSADFNTDPYVREFGIMVKDEMTDVTGRVLQPPSILYGGRNKAIATPVQGVWDMRNKQFHTGIEIKVWAIACFAPQRQCTEVHLKSFTEQLRKISRDAGMPIQGQPCFCKYAQGADSVEPMFRHLKNTYAGLQLVVVILPGKTPVYAEVKRVGDTVLGMATQCVQMKNVQRTTPQTLSNLCLKINVKLGGVNNILLPQGRPPVFQQPVIFLGADVTHPPAGDGKKPSIAAVVGSMDAHPNRYCATVRVQQHRQEIIQDLAAMVRELLIQFYKSTRFKPTRIIFYRDGVSEGQFQQVLHHELLAIREACIKLEKDYQPGITFIVVQKRHHTRLFCTDKNERVGKSGNIPAGTTVDTKITHPTEFDFYLCSHAGIQGTSRPSHYHVLWDDNRFSSDELQILTYQLCHTYVRCTRSVSIPAPAYYAHLVAFRARYHLVDKEHDSAEGSHTSGQSNGRDHQALAKAVQVHQDTLRTMYFA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.153
R work: 0.2375
R free: 0.2697
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 9
Crystallization temperature (K): 293
Crystal growth procedure: PEG 3350, Phenol, Tris, Spermine, Isopropanol
Matthews coefficient: 2.21
Solvent content (%): 44.46
Ligand: PHENOL (IPH)
Ligand formula: C6 H6 O
Ligand molecular weight: 94.111
Ligand SMILES: c1ccc(cc1)O
Ligand InChI: InChI=1S/C6H6O/c7-6-4-2-1-3-5-6/h1-5,7H
Release date: 2016-07-20
Crystal structure of PTPN11 tandem SH2 domains in complex with a TXNIP peptide (PDB entry 5DF6)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 11
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 255 residues
Sequence: GSSHHHHHHSSGRRASVENLYFQGSGRAMTSRRWFHPNITGVEAENLLLTRGVDGSFLARPSKSNPGDFTLSVRRNGAVTHIKIQNTGDYYDLYGGEKFATLAELVQYYMEHHGQLKEKNGDVIELKYPLNCADPTSERWFHGHLSGKEAEKLLTEKGKHGSFLVRESQSHPGDFVLSVRTGDDKGESNDGKSKVTHVMIRCQELKYDVGGGERFDSLTDLVEHYKKNPMVETLGTVLQLKQPLNTTRINLINEF
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.78
R work: 0.194
R free: 0.248
Average B factor: 30.51
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 291
Crystal growth procedure: 20% PEG-3350, 0.2 M ammonium formate
Matthews coefficient: 1.98
Solvent content (%): 37.9
Ligand: UNKNOWN ATOM OR ION (UNX)
Ligand formula: X
Ligand SMILES: *
Release date: 2015-09-23