satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of BACE complex with BMC004 (PDB entry 5QD6)
Macromolecule: Beta-secretase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.23.46
Sequence length: 402 residues
Sequence: GPDEEPEEPGRRGSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYNI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.51
R work: 0.163
R free: 0.203
Average B factor: 57.48
Crystallization method: hanging drop
Crystallization temperature (K): 292
Crystal growth procedure: CRYSTALS WERE GROWN AT 19C BY VAPOUR DIFFUSION IN HANGING DROPS FROM 1.0M AMMONIUM SULFATE. PROTEIN STOCK WAS BACE
MUT46B BATCH XII 8.45MG/ML IN 10MM TRIS-HCL PH 7.4, 25MM NACL, WITH A 5-FOLD EXCESS OF BMC004 ADDED FROM A 50MM STOCK
SOLUTION IN 90% DMSO, 10% H2O (1.8% DMSO IN DROP). CRYO-PROTECTANT WAS 1.2M AMMONIUM SULFATE, 25%(V/V) GLYCEROL, 1.8%
DMSO, 1MM BMC004.
Matthews coefficient: 3.01
Solvent content (%): 59.1
Ligand: (3S,14R,16S)-16-[1,1-dihydroxy-2-({[3-(propan-2-yl)phenyl]methyl}amino)ethyl]-3,4,14-trimethyl-1,4-diazacyclohexadecane-2,5-dione (E6S)
Ligand formula: C29 H49 N3 O4
Ligand molecular weight: 503.717
Ligand SMILES: CC1CCCCCCCCC(=O)N(C(C(=O)NC(C1)C(CNCc2cccc(c2)C(C)C)(O)O)C)C
Ligand InChI: InChI=1S/C29H49N3O4/c1-21(2)25-15-12-14-24(18-25)19-30-20-29(35,36)26-17-22(3)13-10-8-6-7-9-11-16-27(33)32(5)23(4)28(34)31-26/h12,14-15,18,21-23,26,30,35-36H,6-11,13,16-17,19-20H2,1-5H3,(H,31,34)/t22-,23+,26+/m1/s1
Release date: 2020-06-03
Crystal structure of the WD40-repeat of RFWD3 (PDB entry 6CVZ)
Macromolecule: E3 ubiquitin-protein ligase RFWD3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.27
Sequence length: 351 residues
Sequence: GSPSSQGQHKHKYHFQKTFTVSQAGNCRIMAYCDALSCLVISQPSPQASFLPGFGVKMLSTANMKSSQYIPMHGKQIRGLAFSSYLRGLLLSASLDNTIKLTSLETNTVVQTYNAGRPVWSCCWCLDEANYIYAGLANGSILVYDVRNTSSHVQELVAQKARCPLVSLSYMPRAASAAFPYGGVLAGTLEDASFWEQKMDFSHWPHVLPLEPGGCIDFQTENSSRHCLVTYRPDKNHTTIRSVLMEMSYRLDDTGNPICSCQPVHTFFGGPTCKLLTKNAIFQSPENDGNILVCTGDEAANSALLWDAASGSLLQDLQTDQPVLDICPFEVNRNSYLATLTEKMVHIYKWE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.2143
R free: 0.2387
Average B factor: 35.75
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 295
Crystal growth procedure: 16% PEG 3500, 0.2 M Magnesium Chloride, 0.1 M Tris pH8.0
Matthews coefficient: 2.32
Solvent content (%): 47.08
Ligand: MAGNESIUM ION (MG)
Ligand formula: Mg
Ligand molecular weight: 24.305
Ligand SMILES: [Mg+2]
Ligand InChI: InChI=1S/Mg/q+2
Release date: 2018-06-27
USP7 in complex with Cpd2 (4-(3-(1-methylpiperidin-4-yl)-1,2,4-oxadiazol-5-yl)phenol) (PDB entry 5WHC)
Macromolecule: Ubiquitin carboxyl-terminal hydrolase 7
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.19.12
Sequence length: 346 residues
Sequence: KHTGYVGLKNQGATCYMNSLLQTLFFTNQLRKAVYMMPTEGDDSSKSVPLALQRVFYELQHSDKPVGTKKLTKSFGWETLDSFMQHDVQELCRVLLDNVENKMKGTCVEGTIPKLFRGKMVSYIQCKEVDYRSDRREDYYDIQLSIKGKKNIFESFVDYVAVEQLDGDNKYDAGEHGLQEAEKGVKFLTLPPVLHLQLMRFMYDPQTDQNIKINDRFEFPEQLPLDEFLQKTDPKDPANYILHAVLVHSGDNHGGHYVVYLNPKGDGKWCKFDDDVVSRCTKEEAIEHNYGGHDDDLSVRHCTNAYMLVYIRESKLSEVLQAVTDHDIPQQLVERLQEEKRIEAQK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.548
R work: 0.2087
R free: 0.2603
Average B factor: 74.0695
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 289
Crystal growth procedure: PEG 1000, 0.1M Tris-HCl 7.0
Matthews coefficient: 2.59
Solvent content (%): 52.59
Ligand: 4-[3-(1-methylpiperidin-4-yl)-1,2,4-oxadiazol-5-yl]phenol (AJJ)
Ligand formula: C14 H17 N3 O2
Ligand molecular weight: 259.304
Ligand SMILES: CN1CCC(CC1)c2nc(on2)c3ccc(cc3)O
Ligand InChI: InChI=1S/C14H17N3O2/c1-17-8-6-10(7-9-17)13-15-14(19-16-13)11-2-4-12(18)5-3-11/h2-5,10,18H,6-9H2,1H3
Release date: 2017-12-13
SMYD2 in complex with small molecule inhibitor compound-2 (PDB entry 5ARF)
Macromolecule: N-LYSINE METHYLTRANSFERASE SMYD2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1
Sequence length: 433 residues
Sequence: GRAEGLGGLERFCSPGKGRGLRALQPFQVGDLLFSCPAYAYVLTVNERGNHCEYCFTRKEGLSKCGRCKQAFYCNVECQKEDWPMHKLECSPMVVFGENWNPSETVRLTARILAKQKIHPERTPSEKLLAVKEFESHLDKLDNEKKDLIQSDIAALHHFYSKHLGFPDNDSLVVLFAQVNCNGFTIEDEELSHLGSAIFPDVALMNHSCCPNVIVTYKGTLAEVRAVQEIKPGEEVFTSYIDLLYPTEDRNDRLRDSYFFTCECQECTTKDKDKAKVEIRKLSDPPKAEAIRDMVRYARNVIEEFRRAKHYKSPSELLEICELSQEKMSSVFEDSNVYMLHMMYQAMGVCLYMQDWEGALQYGQKIIKPYSKHYPLYSLNVASMWLKLGRLYMGLEHKAAGEKALKKAIAIMEVAHGKDHPYISEIKQEIESH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.92
R work: 0.25747
R free: 0.30052
Average B factor: 52.97
Crystallization pH: 7
Crystal growth procedure: SMYD2 CO-CRYSTALLIZED WITH 2 MMOL SAM. RESERVOIR 23% PEG 3350, 100 MMOL HEPES PH 7.0. CO-COMPLEX WITH INHIBITOR FORMED BY SOAKING SMYD2-SAM CRYSTALS WITH 5 MILLIMOLAR COMPOUND-2 FOR 1 HOUR. CRYO WITH ADDITIONAL 20% GLYCEROL AND 1 MMOL COMPOUND-2.
Matthews coefficient: 2.41
Solvent content (%): 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: 2016-04-27
PanDDA analysis group deposition -- Crystal Structure of JMJD1B in complex with DA000165b (PDB entry 5RAU)
Macromolecule: Lysine-specific demethylase 3B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 372 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSMTSHSWLCDGRLLCLHDPSNKNNWKIFRECWKQGQPVLVSGVHKKLKSELWKPEAFSQEFGDQDVDLVNCRNCAIISDVKVRDFWDGFEIICKRLRSEDGQPMVLKLKDWPPGEDFRDMMPTRFEDLMENLPLPEYTKRDGRLNLASRLPSYFVRPDLGPKMYNAYGLITAEDRRVGTTNLHLDVSDAVNVMVYVGIPIGEGAHDEEVLKTIDEGDADEVTKERIHDHKEKPGALWHIYAAKDAEKIRELLRKVGEEQGQENPPDHDPIHDQSWYLDQTLRKRLYEEYGVQGWAIVQFLGDAVFIPAGAPHQVHNLYSCIKVAEDFVSPEHVKHCFRLTQEFRHLSNTHT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.73
R work: 0.177
R free: 0.2086
Average B factor: 31.732
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M bis-tris pH 5.5 21% PEG3350  0.3M magnesium chloride
Matthews coefficient: 2.79
Solvent content (%): 55.89
Ligand: ethyl 1-pyrazin-2-ylpiperidine-4-carboxylate (HGE)
Ligand formula: C12 H17 N3 O2
Ligand molecular weight: 235.282
Ligand SMILES: CCOC(=O)C1CCN(CC1)c2cnccn2
Ligand InChI: InChI=1S/C12H17N3O2/c1-2-17-12(16)10-3-7-15(8-4-10)11-9-13-5-6-14-11/h5-6,9-10H,2-4,7-8H2,1H3
Release date: 2020-04-22
Structure of Get3 bound to the transmembrane domain of Nyv1 (PDB entry 4XVU)
Macromolecule: ATPase GET3
Type: Protein, polypeptide(L)
Source organism: Saccharomyces cerevisiae S288C
EC number: 3.6
Sequence length: 354 residues
Sequence: MDLTVEPNLHSLITSTTHKWIFVGGKGGVGKTTSSCSIAIQMALSQPNKQFLLISTNPAHNLSDAFGEKFGKDARKVTGMNNLSCMEIDPSAALKDMNDMAVSRANNNGSDGQGDDLGSLLQGGALADLTGSIPGIDEALSFMEVMKHIKRQEQGEGETFDTVIFDTAPTGHTLRFLQLPNTLSKLLEKFGEITNKLGPMLNSFMGAGNVDISGKLNELKANVETIRQQFTDPDLTTFVCVCISEFLSLYETERLIQELISYDMDVNSIIVNQLLFAENDQEHNCKRCQARWKMQKKYLDQIDELYEDFHVVKMPLCAGEIRGLNNLTKFSQFLNKEYNPITDGKVIYELEDKE
Oligomeric state: Hetero 14-mer
Stoichiometry: A4, B4, C4, D1, E1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.35
R work: 0.1971
R free: 0.2335
Average B factor: 67.0967
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 15% PEG 3350, 25 mM succinic acid pH 7.0
Matthews coefficient: 2.25
Solvent content (%): 45.36
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: 2015-03-18
In vitro Crystal Structure of PAK4 in complex with Inka peptide (PDB entry 4XBU)
Macromolecule: Serine/threonine-protein kinase PAK 4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 326 residues
Sequence: MAEEHHHHHHHHLEVLFQGPPPGPRSPQREPQRVSHEQFRAALQLVVDPGDPRSYLDNFIKIGEGSTGIVCIATVRSSGKLVAVKKMDLRKQQRRELLFNEVVIMRDYQHENVVEMYNSYLVGDELWVVMEFLEGGALTDIVTHTRMNEEQIAAVCLAVLQALSVLHAQGVIHRDIKSDSILLTHDGRVKLSDFGFCAQVSKEVPRRKSLVGTPYWMAPELISRLPYGPEVDIWSLGIMVIEMVDGEPPYFNEPPLKAMKMIRDNLPPRLKNLHKVSPSLKGFLDRLLVRDPAQRATAAELLKHPFLAKAGPPASIVPLMRQNRTR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.06
R work: 0.19856
R free: 0.24343
Average B factor: 40.805
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 298.15
Crystal growth procedure: Tris-HCl, PEG 8000
Matthews coefficient: 2.5
Solvent content (%): 50.77
Release date: 2015-12-02
Kinase domain of mutant human ULK1 in complex with compound CCT241533 (PDB entry 8P5H)
Macromolecule: Serine/threonine-protein kinase ULK1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 284 residues
Sequence: SMEPGRGGTETVGKFEFSRKDLIGHGAFAVVFKGRHREKHDLEVAVKCINKKNLAKSQTLLGKEIKILKELKHENIVALYDFQEMANSVYLVMEYCNGGDLADYLHAMRTLSEDTIRLFLQQIAGAMRLLHSKGIIHRDLKPQNILLSNPAGRRANPNSIRVKIADFGFARYLQSNMMAATLCGSPMYMAPEVIMSQHYDGKADLWSIGTIVYQCLTGKAPFQASSPQDLRLFYEKNKTLVPTIPAATSAPLRQLLLALLQRNHKDRMDFDEFFHHPFLDASPS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.941
R work: 0.1698
R free: 0.193
Average B factor: 35.553
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 277.15
Crystal growth procedure: 0.3-0.8 M NaAcetate pH 6, 20-26% w/v PEG3350
Matthews coefficient: 3.46
Solvent content (%): 64.49
Ligand: 4-FLUORO-2-(4-{[(3S,4R)-4-(1-HYDROXY-1-METHYLETHYL)PYRROLIDIN-3-YL]AMINO}-6,7-DIMETHOXYQUINAZOLIN-2-YL)PHENOL (XBJ)
Ligand formula: C23 H27 F N4 O4
Ligand molecular weight: 442.483
Ligand SMILES: CC(C)(C1CNCC1Nc2c3cc(c(cc3nc(n2)c4cc(ccc4O)F)OC)OC)O
Ligand InChI: InChI=1S/C23H27FN4O4/c1-23(2,30)15-10-25-11-17(15)27-21-13-8-19(31-3)20(32-4)9-16(13)26-22(28-21)14-7-12(24)5-6-18(14)29/h5-9,15,17,25,29-30H,10-11H2,1-4H3,(H,26,27,28)/t15-,17-/m1/s1
Release date: 2024-06-05
uPA-HMA (PDB entry 5ZA7)
Macromolecule: Urokinase-type plasminogen activator chain B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.73
Sequence length: 253 residues
Sequence: IIGGEFTTIENQPWFAAIYRRHRGGSVTYVCGGSLISPCWVISATHCFIDYPKKEDYIVYLGRSRLNSNTQGEMKFEVENLILHKDYSADTLAHHNDIALLKIRSKEGRCAQPSRTIQTIALPSMYNDPQFGTSCEITGFGKEQSTDYLYPEQLKMTVVKLISHRECQQPHYYGSEVTTKMLCAADPQWKTDSCQGDSGGPLVCSLQGRMTLTGIVSWGRGCALKDKPGVYTRVSHFLPWIRSHTKEENGLAL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.198
R free: 0.227
Average B factor: 29.47
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 50mM sodium citrate pH 4.6, 1.95M (NH4)2SO4, 0.03% NaN3, 5% PEG 400
Matthews coefficient: 2.13
Solvent content (%): 42.36
Ligand: 3-azanyl-5-(azepan-1-yl)-N-[bis(azanyl)methylidene]-6-chloranyl-pyrazine-2-carboxamide (HMX)
Ligand formula: C12 H18 Cl N7 O
Ligand molecular weight: 311.771
Ligand SMILES: C1CCCN(CC1)c2c(nc(c(n2)N)C(=O)N=C(N)N)Cl
Ligand InChI: InChI=1S/C12H18ClN7O/c13-8-10(20-5-3-1-2-4-6-20)18-9(14)7(17-8)11(21)19-12(15)16/h1-6H2,(H2,14,18)(H4,15,16,19,21)
Release date: 2018-12-19
Structure of PP1 alpha phosphatase bound to ASPP2 (PDB entry 6GHM)
Macromolecule: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.16
Sequence length: 329 residues
Sequence: GHMGSLNLDSIIGRLLEVQGSRPGKNVQLTENEIRGLCLKSREIFLSQPILLELEAPLKICGDIHGQYYDLLRLFEYGGFPPESNYLFLGDYVDRGKQSLETICLLLAYKIKYPENFFLLRGNHECASINRIYGFYDECKRRYNIKLWKTFTDCFNCLPIAAIVDEKIFCCHGGLSPDLQSMEQIRRIMRPTDVPDQGLLCDLLWSDPDKDVQGWGENDRGVSFTFGAEVVAKFLHKHDLDLICRAHQVVEDGYEFFAKRQLVTLFSAPNYCGEFDNAGAMMSVDETLMCSFQILKPADKNKGKYGQFSGLNPGGRPITPPRNSAKAKK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.15
R work: 0.1769
R free: 0.2145
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M TRIS pH 8.5
16 % PEG 8000
Matthews coefficient: 2.67
Solvent content (%): 53.89
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: 2019-02-27
Crystal structure of human Naa50 in complex with AcCoA and an inhibitor (compound 4b) identified using DNA encoded library technology (PDB entry 6WFO)
Macromolecule: N-alpha-acetyltransferase 50
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.258
Sequence length: 171 residues
Sequence: GSMKGSRIELGDVTPHNIKQLKRLNQVIFPVSYNDKFYKDVLEVGELAKLAYFNDIAVGAVCCRVDHSQNQKRLYIMTLGCLAPYRRLGIGTKMLNHVLNICEKDGTFDNIYLHVQISNESAIDFYRKFGFEIIETKKNYYKRIEPADAHVLQKNLKVPSGQNADVQKTDN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.85
R work: 0.202
R free: 0.24
Average B factor: 37.24
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.77
Crystallization temperature (K): 294
Crystal growth procedure: Naa50 apo protein (13.0 mg/ml) was incubated with 4b and AcCoA in a 1:3:3 molar ratio on ice for 60 min.  Reservoir solution of 0.1 M Bis_tris, pH 5.77 and 24% w/v PEG 3350 was mixed 0.2ul:0.2ul with Naa50:4b:AcCoA complex
Matthews coefficient: 2.71
Solvent content (%): 54.67
Ligand: ACETYL COENZYME *A (ACO)
Ligand formula: C23 H38 N7 O17 P3 S
Ligand molecular weight: 809.571
Ligand SMILES: CC(=O)SCCNC(=O)CCNC(=O)C(C(C)(C)COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)O
Ligand InChI: InChI=1S/C23H38N7O17P3S/c1-12(31)51-7-6-25-14(32)4-5-26-21(35)18(34)23(2,3)9-44-50(41,42)47-49(39,40)43-8-13-17(46-48(36,37)38)16(33)22(45-13)30-11-29-15-19(24)27-10-28-20(15)30/h10-11,13,16-18,22,33-34H,4-9H2,1-3H3,(H,25,32)(H,26,35)(H,39,40)(H,41,42)(H2,24,27,28)(H2,36,37,38)/t13-,16-,17-,18+,22-/m1/s1
Release date: 2020-07-01
The phosphatase and C2 domains of SHIP1 with covalent Z1742148362 (PDB entry 8PDH)
Macromolecule: Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.86
Sequence length: 463 residues
Sequence: SMEQPEPDMITIFIGTWNMGNAPPPKKITSWFLSKGQGKTRDDSADYIPHDIYVIGTQEDPLSEKEWLEILKHSLQEITSVTFKTVAIHTLWNIRIVVLAKPEHENRISHICTDNVKTGIANTLGNKGAVGVSFMFNGTSLGFVNSHLTSGSEKKLRRNQNYMNILRFLALGDKKLSPFNITHRFTHLFWFGDLNYRVDLPTWEAETIIQKIKQQQYADLLSHDQLLTERREQKVFLHFEEEEITFAPTYRFERLTRDKYAYTKQKATGMKYNLPSWCDRVLWKSYPLVHVVCQSYGSTSDIMTSDHSPVFATFEAGVTSQFVSKNGPGTVDSQGQIEFLRCYATLKTKSQTKFYLEFHSSCLESFVKSQEGENEEGSEGELVVKFGETLPKLKPIISDPEYLLDQHILISIKSSDSDESYGEGCIALRLEATETQLPIYTPLTHHGELTGHFQGEIKLQTSQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.45
R work: 0.144
R free: 0.2018
Average B factor: 20.658
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 30 mM sodium nitrate, 30 mM dibasic sodium phosphate, 30 mM ammonium sulphate, 100 mM MES/imidazole, 20 % PEG 500 MME, 10% PEG 20,000
Matthews coefficient: 2.09
Solvent content (%): 41.18
Ligand: (5-phenyl-1,3,4-oxadiazol-2-yl)methanimine (YBU)
Ligand formula: C9 H7 N3 O
Ligand molecular weight: 173.171
Ligand SMILES: c1ccc(cc1)c2nnc(o2)C=N
Ligand InChI: InChI=1S/C9H7N3O/c10-6-8-11-12-9(13-8)7-4-2-1-3-5-7/h1-6,10H/b10-6-
Release date: 2023-06-28
Binary complex of human DNA Polymerase Mu with MnATP (PDB entry 6AEC)
Macromolecule: DNA-directed DNA/RNA polymerase mu
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 356 residues
Sequence: GSAAAPLSPAWMPAYACQRPTPLTHHNTGLSEALEILAEAAGFEGSEGRLLTFCRAASVLKALPSPVTTLSQLQGLPHFGEHSSRVVQELLEHGVCEEVERVRRSERYQTMKLFTQIFGVGVKTADRWYREGLRTLDDLREQPQKLTQQQKAGLQHHQDLSTPVLRSDVDALQQVVEEAVGQALPGATVTLTGGFRRGKLQGHDVDFLITHPKEGQEAGLLPRVMCRLQDQGLILYHQHQHSCCESPTRLAQQSHMDAFERSFCIFRLPQPGSWKAVRVDLVVAPVSQFPFALLGWTGSKLFQRELRRFSRKEKGLWLNSHGLFDPEQKTFFQAASEEDIFRHLGLEYLPPEQRNA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.72
R work: 0.19146
R free: 0.22215
Average B factor: 20.151
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 298
Crystal growth procedure: 0.1 M HEPES pH 7.5, 1.5 M Li2SO4
Matthews coefficient: 2.47
Solvent content (%): 50.16
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: 2019-05-29
PanDDA analysis group deposition -- Crystal Structure of DCP2 (NUDT20) in complex with FMOPL000144a (PDB entry 5QOO)
Macromolecule: DCP2 (NUDT20)
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.62
Sequence length: 167 residues
Sequence: SMGVPTYGAIILDETLENVLLVQGYLAKSGWGFPKGKVNKEEAPHDCAAREVFEETGFDIKDYICKDDYIELRINDQLARLYIIPGIPKDTKFNPKTRREIRNIEWFSIEKLPCHRNDMTPKSKLGLAPNKFFMAIPFIRPLRDWLSRRFGDSSDSDNGFSSTGSTP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.56
R work: 0.2023
R free: 0.2521
Average B factor: 35.528
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 4.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M acetate, pH 4.5, 5-25% PEG3350
Matthews coefficient: 2.58
Solvent content (%): 52.3
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: 2019-05-08
Structure of human cathepsin K in complex with the selective activity-based probe Gu3416 (PDB entry 7NXM)
Macromolecule: Cathepsin K
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.22.38
Sequence length: 216 residues
Sequence: RAPDSVDYRKKGYVTPVKNQGQCGSCWAFSSVGALEGQLKKKTGKLLNLSPQNLVDCVSENDGCGGGYMTNAFQYVQKNRGIDSEDAYPYVGQEESCMYNPTGKAAKCRGYREIPEGNEKALKRAVARVGPVSVAIDASLTSFQFYSKGVYYDESCNSDNLNHAVLAVGYGIQKGNKHWIIKNSWGENWGNKGYILMARNKNNACGIANLASFPKM
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.72
R work: 0.1602
R free: 0.1784
Average B factor: 17.819
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 291
Crystal growth procedure: Composition of reservoir solution was 0.1 M MES/imidazole buffer, containing: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD 0.03 M of each NPS (a mix containing sodium nitrate, disodium hydrogen phosphate and ammonium sulfate) additives, pH 6.5.
Morpheus C4 condition
Matthews coefficient: 1.963
Solvent content (%): 37.38
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: 2021-09-08
Crystal structure of the N-terminal domain single mutant (D119A) of the human mitochondrial calcium uniporter fused with T4 lysozyme (PDB entry 6KVX)
Macromolecule: Endolysin,Calcium uniporter protein, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Tequatrovirus T4
EC number: 3.2.1.17
Sequence length: 261 residues
Sequence: MNIFEMLRIDEGLRLKIYKNTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYGSVTVVYQNGLPVISVRLPSRRERCQFTLKPISDSVGVFLRQLQEEARGIDRVAIYSPDGVRVAASTGIDLLLLDDFKLVINDLTYHVRPPKLEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.85
R work: 0.1795
R free: 0.26218
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 20% (w/v) polyethylene glycol (PEG) 3350, 5% (v/v) glycerol, 0.3 M (NH4)2SO4, and 0.1 M Bis-Tris-HCl (pH 5.5)
Matthews coefficient: 2.99
Solvent content (%): 58.85
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: 2020-05-27
Pre-catalytic ternary complex of human DNA Polymerase Mu with 1-nt gapped substrate containing template 8OG and bound CMPCPP (PDB entry 6P1T)
Macromolecule: DNA-directed DNA/RNA polymerase mu
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 354 residues
Sequence: GSAAASPAWMPAYACQRPTPLTHHNTGLSEALEILAEAAGFEGSEGRLLTFCRAASVLKALPSPVTTLSQLQGLPHFGEHSSRVVQELLEHGVCEEVERVRRSERYQTMKLFTQIFGVGVKTADRWYREGLRTLDDLREQPQKLTQQQKAGLQHHQDLSTPVLRSDVDALQQVVEEAVGQALPGATVTLTGGFRRGKLQGHDVDFLITHPKEGQEAGLLPRVMCRLQDQGLILYHQHQHSCCESPTRLAQQSHMDAFERSFCIFRLPQPGSWKAVRVDLVVAPVSQFPFALLGWTGSKLFQRELRRFSRKEKGLWLNSHGLFDPEQKTFFQAASEEDIFRHLGLEYLPPEQRNA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.1692
R free: 0.1909
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 94mM HEPES pH 7.5, 94mM NaCl, 9.4% w/v PEG4000
Matthews coefficient: 2.85
Solvent content (%): 56.9
Ligand: 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine (2TM)
Ligand formula: C10 H18 N3 O13 P3
Ligand molecular weight: 481.184
Ligand SMILES: C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(CP(=O)(O)OP(=O)(O)O)O)O)O
Ligand InChI: InChI=1S/C10H18N3O13P3/c11-6-1-2-13(10(16)12-6)9-8(15)7(14)5(25-9)3-24-27(17,18)4-28(19,20)26-29(21,22)23/h1-2,5,7-9,14-15H,3-4H2,(H,17,18)(H,19,20)(H2,11,12,16)(H2,21,22,23)/t5-,7-,8-,9-/m1/s1
Release date: 2019-09-04
INPP5D PanDDA analysis group deposition -- Crystal Structure of the phosphatase and C2 domains of SHIP1 in complex with Z198194394 (PDB entry 5RY6)
Macromolecule: Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.86
Sequence length: 463 residues
Sequence: SMEQPEPDMITIFIGTWNMGNAPPPKKITSWFLSKGQGKTRDDSADYIPHDIYVIGTQEDPLSEKEWLEILKHSLQEITSVTFKTVAIHTLWNIRIVVLAKPEHENRISHICTDNVKTGIANTLGNKGAVGVSFMFNGTSLGFVNSHLTSGSEKKLRRNQNYMNILRFLALGDKKLSPFNITHRFTHLFWFGDLNYRVDLPTWEAETIIQKIKQQQYADLLSHDQLLTERREQKVFLHFEEEEITFAPTYRFERLTRDKYAYTKQKATGMKYNLPSWCDRVLWKSYPLVHVVCQSYGSTSDIMTSDHSPVFATFEAGVTSQFVSKNGPGTVDSQGQIEFLRCYATLKTKSQTKFYLEFHSSCLESFVKSQEGENEEGSEGELVVKFGETLPKLKPIISDPEYLLDQHILISIKSSDSDESYGEGCIALRLEATETQLPIYTPLTHHGELTGHFQGEIKLQTSQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.74
R work: 0.1768
R free: 0.2157
Average B factor: 23.762
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 30 mM sodium nitrate, 30 mM dibasic sodium phosphate, 30 mM ammonium sulfate, 100 mM MES/imidazole, pH 6.5, 20% PEG500 MME, 10% PEG20000
Matthews coefficient: 2.09
Solvent content (%): 41.2
Ligand: 4-(4-fluorophenyl)piperazine-1-carboxamide (O1M)
Ligand formula: C11 H14 F N3 O
Ligand molecular weight: 223.247
Ligand SMILES: c1cc(ccc1N2CCN(CC2)C(=O)N)F
Ligand InChI: InChI=1S/C11H14FN3O/c12-9-1-3-10(4-2-9)14-5-7-15(8-6-14)11(13)16/h1-4H,5-8H2,(H2,13,16)
Release date: 2020-11-11