satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of human SDHA-SDHAF2-SDHAF4 assembly intermediate (PDB entry 8DYD)
Macromolecule: Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.3.5.1
Sequence length: 632 residues
Sequence: MRGSHHHHHHGSAKVSDSISAQYPVVDHEFDAVVVGAGGAGLRAAFGLSEAGFNTACVTKLFPTRSHTVAAQGGINAALGNMEEDNWRWHFYDTVKGSDWLGDQDAIHYMTEQAPAAVVELENYGMPFSRTEDGKIYQRAFGGQSLKFGKGGQAHRCCCVADRTGHSLLHTLYGRSLRYDTSYFVEYFALDLLMENGECRGVIALCIEDGSIHRIRAKNTVVATGGYGRTYFSCTSAHTSTGDGTAMITRAGLPCQDLEFVQFHPTGIYGAGCLITEGCRGEGGILINSQGERFMERYAPVAKDLASRDVVSRSMTLEIREGRGCGPEKDHVYLQLHHLPPEQLATRLPGISETAMIFAGVDVTKEPIPVLPTVHYNMGGIPTNYKGQVLRHVNGQDQIVPGLYACGEAACASVHGANRLGANSLLDLVVFGRACALSIEESCRPGDKVPPIKPNAGEESVMNLDKLRFADGSIRTSELRLSMQKSMQNHAAVFRVGSVLQEGCGKISKLYGDLKHLKTFDRGMVWNTDLVETLELQNLMLCALQTIYGAEARKESRGAHAREDYKVRIDEYDYSKPIQGQQKKPFEEHWRKHTLSYVDVGTGKVTLEYRPVIDKTLNEADCATVPPAIRSY
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.52
R work: 0.1567
R free: 0.1842
Average B factor: 24.06
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 298
Crystal growth procedure: 200 mM Ammonium citrate tribasic pH 7.0, 20% w/v Polyethylene glycol 3,350
Matthews coefficient: 2.2
Solvent content (%): 44.07
Ligand: FLAVIN-ADENINE DINUCLEOTIDE (FAD)
Ligand formula: C27 H33 N9 O15 P2
Ligand molecular weight: 785.55
Ligand SMILES: Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)O
Ligand InChI: InChI=1S/C27H33N9O15P2/c1-10-3-12-13(4-11(10)2)35(24-18(32-12)25(42)34-27(43)33-24)5-14(37)19(39)15(38)6-48-52(44,45)51-53(46,47)49-7-16-20(40)21(41)26(50-16)36-9-31-17-22(28)29-8-30-23(17)36/h3-4,8-9,14-16,19-21,26,37-41H,5-7H2,1-2H3,(H,44,45)(H,46,47)(H2,28,29,30)(H,34,42,43)/t14-,15+,16+,19-,20+,21+,26+/m0/s1
Release date: 2024-01-10
Human MST3 (STK24) kinase in complex with inhibitor MR39 (PDB entry 8BZI)
Macromolecule: Serine/threonine-protein kinase 24
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 306 residues
Sequence: MRAQLWGLALNKRRATLPHPGGSTNLKADPEELFTKLEKIGKGSFGEVFKGIDNRTQKVVAIKIIDLEEAEDEIEDIQQEITVLSQCDSPYVTKYYGSYLKDTKLWIIMEYLGGGSALDLLEPGPLDETQIATILREILKGLDYLHSEKKIHRDIKAANVLLSEHGEVKLADFGVAGQLTDTQIKRNTFVGTPFWMAPEVIKQSAYDSKADIWSLGITAIELARGEPPHSELHPMKVLFLIPKNNPPTLEGNYSKPLKEFVEACLNKEPSFRPTAKELLKHKFILRNAKKTSYLTELIDAHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.72
R work: 0.15183354662
R free: 0.195790856793
Average B factor: 37.2487699881
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: Protein solution: 11 mg/mL MST3 in 25 mM HEPES pH 7.5, 200 mM NaCl, 0.5 mM TCEP, 5% glycerol, with 1 mM inhibitor).
Crystallization buffer: 20% PEG 3350, 0.1 M bis-tris pH 6.5.
Matthews coefficient: 2.58
Solvent content (%): 52.27
Ligand: 8-(4-azanylbutyl)-6-[2,5-bis(fluoranyl)-4-(6-methylpyridin-2-yl)phenyl]-2-(methylamino)pyrido[2,3-d]pyrimidin-7-one (SJL)
Ligand formula: C24 H24 F2 N6 O
Ligand molecular weight: 450.484
Ligand SMILES: Cc1cccc(n1)c2cc(c(cc2F)C3=Cc4cnc(nc4N(C3=O)CCCCN)NC)F
Ligand InChI: InChI=1S/C24H24F2N6O/c1-14-6-5-7-21(30-14)18-12-19(25)16(11-20(18)26)17-10-15-13-29-24(28-2)31-22(15)32(23(17)33)9-4-3-8-27/h5-7,10-13H,3-4,8-9,27H2,1-2H3,(H,28,29,31)
Release date: 2023-01-18
Carbonic anhydrase II radiation damage RT 31-60 (PDB entry 8SD6)
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): 1.397
R work: 0.1374
R free: 0.1536
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 293
Crystal growth procedure: 1.6 M sodium citrate, 50 mM Tris base
Matthews coefficient: 2.11
Solvent content (%): 41.6
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: 2024-03-13
Crystal structure of MYST acetyltransferase domain in complex with inhibitor 80 (PDB entry 6PDB)
Macromolecule: Histone acetyltransferase KAT8
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 272 residues
Sequence: KYVDKIHIGNYEIDAWYFSPFPEDYGKQPKLWLCEYCLKYMKYEKSYRFHLGQCQWRQPPGKEIYRKSNISVHEVDGKDHKIYCQNLCLLAKLFLDHKTLYFDVEPFVFYILTEVDRQGAHIVGYFSKEKESPDGNNVSCIMILPPYQRRGYGRFLIAFSYELSKLESTVGSPEKPLSDLGKLSYRSYWSSVLLENLRDFRGTLSIKDLSQMTSITQNDIISTLQSLNMVKYWKGQHVICVTPKLVEEHLKSAQYKKPPITVDSVCLKWAPP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.42
R work: 0.1856
R free: 0.2209
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 292
Crystal growth procedure: 27% PEG 3350, 0.2 M ammonium sulfate, 0.1 M bis-tris pH 6.5
Matthews coefficient: 2.5
Solvent content (%): 50.75
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2020-04-01
Crystal structure of human TAK1/TAB1 fusion protein in complex with ligand 11c (PDB entry 5JGA)
Macromolecule: TAK1 kinase - TAB1 chimera fusion protein
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.25
Sequence length: 315 residues
Sequence: GPLHMIDYKEIEVEEVVGRGAFGVVCKAKWRAKDVAIKQIESESERKAFIVELRQLSRVNHPNIVKLYGACLNPVCLVMEYAEGGSLYNVLHGAEPLPYYTAAHAMSWCLQCSQGVAYLHSMQPKALIHRDLKPPNLLLVAGGTVLKICDFGTACDIQTHMTNNKGSAAWMAPEVFEGSNYSEKCDVFSWGIILWEVITRRKPFDEIGGPAFRIMWAVHNGTRPPLIKNLPKPIESLMTRCWSKDPSQRPSMEEIVKIMTHLMRYFPGADEPLQYPCQHSLPPGEDGRVEPYVDFAEFYRLWSVDHGEQSVVTAP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.0
R work: 0.1952
R free: 0.2213
Average B factor: 40.658
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.7
Crystallization temperature (K): 294
Crystal growth procedure: 1.7M sodium potassium phosphate, 20%(v/v) Glycerol as cryoprotectant
Matthews coefficient: 3.86
Solvent content (%): 68.14
Ligand: N-[5-(4-methylpiperazine-1-carbonyl)[1,1'-biphenyl]-2-yl]-4-oxo-3,4-dihydrothieno[3,2-d]pyrimidine-7-carboxamide (6KC)
Ligand formula: C25 H23 N5 O3 S
Ligand molecular weight: 473.547
Ligand SMILES: CN1CCN(CC1)C(=O)c2ccc(c(c2)c3ccccc3)NC(=O)c4csc5c4N=CNC5=O
Ligand InChI: InChI=1S/C25H23N5O3S/c1-29-9-11-30(12-10-29)25(33)17-7-8-20(18(13-17)16-5-3-2-4-6-16)28-23(31)19-14-34-22-21(19)26-15-27-24(22)32/h2-8,13-15H,9-12H2,1H3,(H,28,31)(H,26,27,32)
Release date: 2016-07-27
Matrix metalloproteinase-13 complexed with selective inhibitor compound (S)-17a (PDB entry 5UWL)
Macromolecule: Collagenase 3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.24
Sequence length: 172 residues
Sequence: MYNVFPRTLKWSKMNLTYRIVNYTPDMTHSEVEKAFKKAFKVWSDVTPLNFTRLHDGIADIMISFGIKEHGDFYPFDGPSGLLAHAFPPGPNYGGDAHFDDDETWTSSSKGYNLFLVAAHEFGHSLGLDHSKDPGALMFPIYTYTGKSHFMLPDDDVQGIQSLYGPGDEDPN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.55
R work: 0.1988
R free: 0.2395
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 277
Crystal growth procedure: 0.2 M sodium chloride, 0.1 M Tris pH 7, 1.0 M sodium citrate
Matthews coefficient: 4.47
Solvent content (%): 72.49
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: 2017-07-12
Crystal structure of the WDR domain of human DCAF1 in complex with OICR-8268 compound (PDB entry 8F8E)
Macromolecule: DDB1- and CUL4-associated factor 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 315 residues
Sequence: GASAFRPISVFREANEDESGFTCCAFSARERFLMLGTCTGQLKLYNVFSGQEEASYNCHNSAITHLEPSRDGSLLLTSATWSQPLSALWGMKSVFDMKHSFTEDHYVEFSKHSQDRVIGTKGDIAHIYDIQTGNKLLTLFNPDLANNYKRNCATFNPTDDLVLNDGVLWDVRSAQAIHKFDKFNMNISGVFHPNGLEVIINTEIWDLRTFHLLHTVPALDQCRVVFNHTGTVMYGAMLQADDEDDLMEERMKSPFGSSFRTFNATDYKPIATIDVKRNIFDLCTDTKDCYLAVIENQGSMDALNMDTVCRLYEVG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.55
R work: 0.18123
R free: 0.20898
Average B factor: 22.966
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 20% PEG3350, 0.2M di-Ammonium Citrate
Matthews coefficient: 2.2
Solvent content (%): 44.21
Ligand: (3P)-N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-3-(4-chloro-2-fluorophenyl)-1H-pyrazole-4-carboxamide (XJI)
Ligand formula: C19 H14 Cl2 F2 N4 O2
Ligand molecular weight: 439.243
Ligand SMILES: c1cc(c(cc1C(CC(=O)N)NC(=O)c2c[nH]nc2c3ccc(cc3F)Cl)Cl)F
Ligand InChI: InChI=1S/C19H14Cl2F2N4O2/c20-10-2-3-11(15(23)6-10)18-12(8-25-27-18)19(29)26-16(7-17(24)28)9-1-4-14(22)13(21)5-9/h1-6,8,16H,7H2,(H2,24,28)(H,25,27)(H,26,29)/t16-/m0/s1
Release date: 2023-03-01
Crystal structure of the UBE2A variant Q93E (PDB entry 6CYR)
Macromolecule: Ubiquitin-conjugating enzyme E2 A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.23
Sequence length: 155 residues
Sequence: GSHMSTPARRRLMRDFKRLQEDPPAGVSGAPSENNIMVWNAVIFGPEGTPFEDGTFKLTIEFTEEYPNKPPTVRFVSKMFHPNVYADGSICLDILENRWSPTYDVSSILTSIQSLLDEPNPNSPANSQAAQLYQENKREYEKRVSAIVEQSWRDC
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.2038
R free: 0.2492
Average B factor: 55.5488
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 50 mM di-Sodium succinate pH 7.0 and 12-14% PEG 3350
Matthews coefficient: 2.49
Solvent content (%): 50.65
Release date: 2018-12-12
X-ray structure of human PPAR gamma ligand binding domain-bezafibrate co-rystals obtained by co-crystallization (PDB entry 7WGO)
Macromolecule: 15-meric peptide from Nuclear receptor coactivator 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 15 residues
Sequence: LTERHKILHRLLQEG
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.36
R work: 0.1949
R free: 0.2253
Average B factor: 59.158
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M Tris (pH 8.0), 1.1 M trisodium citrate
Matthews coefficient: 2.97
Solvent content (%): 58.63
Ligand: 2-[P-[2-P-CHLOROBENZAMIDO)ETHYL]PHENOXY]-2-METHYLPROPIONIC ACID (PEM)
Ligand formula: C19 H20 Cl N O4
Ligand molecular weight: 361.819
Ligand SMILES: CC(C)(C(=O)O)Oc1ccc(cc1)CCNC(=O)c2ccc(cc2)Cl
Ligand InChI: InChI=1S/C19H20ClNO4/c1-19(2,18(23)24)25-16-9-3-13(4-10-16)11-12-21-17(22)14-5-7-15(20)8-6-14/h3-10H,11-12H2,1-2H3,(H,21,22)(H,23,24)
Release date: 2022-05-25
Human Mps1 kinase domain with ordered activation loop (PDB entry 6GVJ)
Macromolecule: Dual specificity protein kinase TTK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 429 residues
Sequence: MAHHHHHHSAALEVLFQGPGPAASSNHWQIPELARKVNTEQKHTTFEQPVFSVSKQSPPISTSKWFDPKSICKTPSSNTLDDYMSCFRTPVVKNDFPPACQLSTPYGQPACFQQQQHQILATPLQNLQVLASSSANECISVKGRIYSILKQIGSGGSSKVFQVLNEKKQIYAIKYVNLEEADNQTLDSYRNEIAYLNKLQQHSDKIIRLYDYEITDQYIYMVMECGNIDLNSWLKKKKSIDPWERKSYWKNMLEAVHTIHQHGIVHSDLKPANFLIVDGMLKLIDFGIANQMQPDTTSVVKDSQVGTVNYMPPEAIKDMSSSRENGKSKSKISPKSDVWSLGCILYYMTYGKTPFQQIINQISKLHAIIDPNHEIEFPDIPEKDLQDVLKCCLKRDPKQRISIPELLAHPYVQIQTHPVNQMAKGTTEE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.41
R work: 0.2012
R free: 0.2334
Average B factor: 50.838
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.2 M Ammonium sulfate
20% (w/v) PEG8000
0.1 M MES-buffer, pH 6.5
Matthews coefficient: 2.07
Solvent content (%): 40.67
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: 2019-01-09
Crystal structure of the human METTL3-METTL14 complex with compound DHU_M3M_154 (PDB entry 7NHJ)
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): 2.16
R work: 0.2175
R free: 0.2746
Average B factor: 49.22
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 295
Crystal growth procedure: 20% PEG 3350, 400mM Mg acetate
Matthews coefficient: 2.17
Solvent content (%): 43.33
Ligand: (S)-3-(((6-(3-(hydroxymethyl)piperidin-1-yl)pyrimidin-4-yl)amino)methyl)benzenesulfonamide (UDW)
Ligand formula: C17 H23 N5 O3 S
Ligand molecular weight: 377.461
Ligand SMILES: c1cc(cc(c1)S(=O)(=O)N)CNc2cc(ncn2)N3CCCC(C3)CO
Ligand InChI: InChI=1S/C17H23N5O3S/c18-26(24,25)15-5-1-3-13(7-15)9-19-16-8-17(21-12-20-16)22-6-2-4-14(10-22)11-23/h1,3,5,7-8,12,14,23H,2,4,6,9-11H2,(H2,18,24,25)(H,19,20,21)/t14-/m1/s1
Release date: 2021-10-20
PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of HAO1 in complex with Z1787627869 (PDB entry 5QID)
Macromolecule: Hydroxyacid oxidase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.1.3.15
Sequence length: 369 residues
Sequence: SMLPRLICINDYEQHAKSVLPKSIYDYYRSGANDEETLADNIAAFSRWKLYPRMLRNVAETDLSTSVLGQRVSMPICVGATAMQRMAHVDGELATVRACQSLGTGMMLSSWATSSIEEVAEAGPEALRWLQLYIYKDREVTKKLVRQAEKMGYKAIFVTVDTPYLGNRLDDVRNRFKLPPQLRMKNFETSTLSFSPEENFGDDSGLAAYVAKAIDPSISWEDIKWLRRLTSLPIVAKGILRGDDAREAVKHGLNGILVSNHGARQLDGVPATIDVLPEIVEAVEGKVEVFLDGGVRKGTDVLKALALGAKAVFVGRPIVWGLAFQGEKGVQDVLEILKEEFRLAMALSGCQNVKVIDKTLVRKNPLAVS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.45
R work: 0.1797
R free: 0.1975
Average B factor: 19.904
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.75
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M MIB pH 5.75 - 7.0, 27.5-35% PEG1000
Matthews coefficient: 2.34
Solvent content (%): 47.42
Ligand: FLAVIN MONONUCLEOTIDE (FMN)
Ligand formula: C17 H21 N4 O9 P
Ligand molecular weight: 456.344
Ligand SMILES: Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)O)O)O)O
Ligand InChI: InChI=1S/C17H21N4O9P/c1-7-3-9-10(4-8(7)2)21(15-13(18-9)16(25)20-17(26)19-15)5-11(22)14(24)12(23)6-30-31(27,28)29/h3-4,11-12,14,22-24H,5-6H2,1-2H3,(H,20,25,26)(H2,27,28,29)/t11-,12+,14-/m0/s1
Release date: 2018-07-18
Ube2V1 in complex with ubiquitin variant Ubv.V1.1 and Ube2N/Ubc13 (PDB entry 6D6I)
Macromolecule: Ubiquitin-conjugating enzyme E2 variant 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 143 residues
Sequence: GSTGVKVPRNFRLLEELEEGQKGVGDGTVSWGLEDDEDMTLTRWTGMIIGPPRTIYENRIYSLKIECGPKYPEAPPFVRFVTKINMNGVNSSNGVVDPRAISVLAKWQNSYSIKVVLQELRRLMMSKENMKLPQPPEGQCYSN
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.551
R work: 0.2635
R free: 0.2963
Average B factor: 114.7371
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.2M LiSO4, 25% PEG3350, 0.1 M Tris-HCl pH 8.5
Matthews coefficient: 2.77
Solvent content (%): 55.58
Release date: 2019-07-17
Crystal structure of DAPK1-genistein complex in the presence of bromide ions. (PDB entry 5AV4)
Macromolecule: Death-associated protein kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 293 residues
Sequence: MTVFRQENVDDYYDTGEELGSGQFAVVKKCREKSTGLQYAAKFIKKRRTKSSRRGVSREDIEREVSILKEIQHPNVITLHEVYENKTDVILILELVAGGELFDFLAEKESLTEEEATEFLKQILNGVYYLHSLQIAHFDLKPENIMLLDRNVPKPRIKIIDFGLAHKIDFGNEFKNIFGTPEFVAPEIVNYEPLGLEADMWSIGVITYILLSGASPFLGDTKQETLANVSAVNYEFEDEYFSNTSALAKDFIRRLLVKDPKKRMTIQDSLQHPWIKPKDTQQALSLEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.4
R work: 0.1894
R free: 0.2276
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 2 M ammonium sulfate, 0.1 M MES
Matthews coefficient: 1.91
Solvent content (%): 35.5
Ligand: GENISTEIN (GEN)
Ligand formula: C15 H10 O5
Ligand molecular weight: 270.237
Ligand SMILES: c1cc(ccc1C2=COc3cc(cc(c3C2=O)O)O)O
Ligand InChI: InChI=1S/C15H10O5/c16-9-3-1-8(2-4-9)11-7-20-13-6-10(17)5-12(18)14(13)15(11)19/h1-7,16-18H
Release date: 2015-10-07
Crystal structure of the human METTL3-METTL14 complex with compound UOZ078 (PDB entry 7NID)
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): 2.3
R work: 0.2023
R free: 0.242
Average B factor: 46.1
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 295
Crystal growth procedure: 20% PEG 3350, 400mM Mg acetate
Matthews coefficient: 2.11
Solvent content (%): 41.77
Ligand: (R)-1-(6-(benzylamino)pyrimidin-4-yl)-3-(((6-((4,4-dimethylpiperidin-1-yl)methyl)naphthalen-1-yl)amino)methyl)piperidin-3-ol (UEZ)
Ligand formula: C35 H44 N6 O
Ligand molecular weight: 564.763
Ligand SMILES: CC1(CCN(CC1)Cc2ccc3c(c2)cccc3NCC4(CCCN(C4)c5cc(ncn5)NCc6ccccc6)O)C
Ligand InChI: InChI=1S/C35H44N6O/c1-34(2)15-18-40(19-16-34)23-28-12-13-30-29(20-28)10-6-11-31(30)37-24-35(42)14-7-17-41(25-35)33-21-32(38-26-39-33)36-22-27-8-4-3-5-9-27/h3-6,8-13,20-21,26,37,42H,7,14-19,22-25H2,1-2H3,(H,36,38,39)/t35-/m1/s1
Release date: 2021-10-20
Ni- Carbonic Anhydrase II pH 7.8 0 atm CO2 (PDB entry 6LV5)
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: 0.1163
R free: 0.141
Average B factor: 11.725
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 293
Crystal growth procedure: 1.3 M sodium citrate, 50 mM Tris-HCl
Matthews coefficient: 2.08
Solvent content (%): 41.01
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: 2020-08-19
DNA Polymerase Lambda, TTP:At Mn2+ Product State Ternary Complex, 60 min (PDB entry 7M4B)
Macromolecule: DNA (5'-D(*CP*GP*GP*CP*AP*GP*TP*AP*CP*TP*G)-3')
Type: DNA, polydeoxyribonucleotide
Source organism: synthetic construct
Sequence length: 11 residues
Sequence: CGGCAGTACTG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.66
R work: 0.1807
R free: 0.2017
Average B factor: 43.5286
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 80-95mM BICINE pH 8.3, 0.3M Na-K Tartrate, 18-22.5% PolyPure PEG
Matthews coefficient: 2.83
Solvent content (%): 56.61
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: 2022-07-06
Human Carbonic Anhydrase II native 15 atm CO2 (PDB entry 6KM6)
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): 1.15
R work: 0.1052
R free: 0.1336
Average B factor: 17.558
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 293
Crystal growth procedure: 1.3 M sodium citrate, 100 mM Tris-HCl
Matthews coefficient: 2.07
Solvent content (%): 40.72
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: 2020-08-05
Crystal structure of p97 N/D1 in complex with a valosin-containing protein methyltransferase (PDB entry 8HL7)
Macromolecule: Protein N-lysine methyltransferase METTL21D
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1
Sequence length: 208 residues
Sequence: MFVRVLEKRDGTVLRLQQYSSGGVGCVVWDAAIVLSKYLETPEFSGDGAHALSRRSVLELGSGTGAVGLMAATLGADVVVTDLEELQDLLKMNINMNKHLVTGSVQAKVLKWGEEVEGFPSPPDFILMADCIYYEESLEPLLKTLKDISGFETCIICCYEQRTMGKNPEIEKKYFELLQLDFDFEKIPLEKHDEEYRSEDIHIIYIRK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.8
R work: 0.2172
R free: 0.2609
Average B factor: 66.14
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 295
Crystal growth procedure: 20 % (w/v) polyethylene glycol (PEG) 3350, 0.1M Na-HEPES (pH 7.5), 2 % (v/v) Tacsimate (pH 7.0), and 3 % (w/v) 6-aminohexanoic acid
Matthews coefficient: 3.16
Solvent content (%): 61.04
Ligand: S-ADENOSYL-L-HOMOCYSTEINE (SAH)
Ligand formula: C14 H20 N6 O5 S
Ligand molecular weight: 384.411
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CSCCC(C(=O)O)N)O)O)N
Ligand InChI: InChI=1S/C14H20N6O5S/c15-6(14(23)24)1-2-26-3-7-9(21)10(22)13(25-7)20-5-19-8-11(16)17-4-18-12(8)20/h4-7,9-10,13,21-22H,1-3,15H2,(H,23,24)(H2,16,17,18)/t6-,7+,9+,10+,13+/m0/s1
Release date: 2023-07-12
Crystal structure of human neprilysin E584D in complex with C-type natriuretic peptide. (PDB entry 6SH2)
Macromolecule: C-type natriuretic peptide fragment (CNP)
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 4 residues
Sequence: AAAA
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.6
R work: 0.2435
R free: 0.2866
Average B factor: 91.557
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 291.15
Crystal growth procedure: Potassium nitrate, Sodium iodide,  PEG 3350
Matthews coefficient: 2.43
Solvent content (%): 49.4
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: 2019-09-25