satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal Structure of human phosphodiesterase 10 in complex with 4-N-(2-methoxyethyl)-4-N,2-dimethyl-3-N-(2-phenylimidazo[1,2-a]pyridin-7-yl)pyrazole-3,4-dicarboxamide (PDB entry 5SGP)
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): 1.95
R work: 0.1716
R free: 0.2142
Average B factor: 33.788
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: 2.64
Solvent content (%): 53.35
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
Structure of cyclophilin A in complex with 3,4-diaminobenzamide (PDB entry 5NOY)
Macromolecule: Peptidyl-prolyl cis-trans isomerase A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 165 residues
Sequence: MVNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFGSRNGKTSKKITIADCGQLE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.43
R work: 0.15743
R free: 0.18247
Average B factor: 18.09
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 279.15
Crystal growth procedure: PEG 8000, Tris-HCl
Matthews coefficient: 2.83
Solvent content (%): 56.49
Ligand: 3,4-bis(azanyl)benzamide (93K)
Ligand formula: C7 H9 N3 O
Ligand molecular weight: 151.166
Ligand SMILES: c1cc(c(cc1C(=O)N)N)N
Ligand InChI: InChI=1S/C7H9N3O/c8-5-2-1-4(7(10)11)3-6(5)9/h1-3H,8-9H2,(H2,10,11)
Release date: 2017-07-12
Human PPARgamma ligand binding dmain complexed with SB1451 in a covalent bonded form (PDB entry 5DV8)
Macromolecule: Peroxisome proliferator-activated receptor gamma
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 287 residues
Sequence: GSHMAEISSDIDQLNPESADLRALAKHLYDSYIKSFPLTKAKARAILTGKTTDKSPFVIYDMNSLMMGEDKIKFKHITPLQEQSKEVAIRIFQGCQFRSVEAVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQEIYKDLY
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.75
R work: 0.1916
R free: 0.24311
Average B factor: 59.267
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 297
Crystal growth procedure: 0.19M sodium acetate trihydrate, 0.1M sodium cacodylate pH 6.5, 26% PEG 8000
Matthews coefficient: 2.72
Solvent content (%): 54.86
Ligand: N-[2-({2-[({4-[(4-methylpiperazin-1-yl)methyl]benzoyl}amino)methyl]benzyl}oxy)phenyl]-3-nitrobenzamide (T51)
Ligand formula: C34 H35 N5 O5
Ligand molecular weight: 593.672
Ligand SMILES: CN1CCN(CC1)Cc2ccc(cc2)C(=O)NCc3ccccc3COc4ccccc4NC(=O)c5cccc(c5)[N+](=O)[O-]
Ligand InChI: InChI=1S/C34H35N5O5/c1-37-17-19-38(20-18-37)23-25-13-15-26(16-14-25)33(40)35-22-28-7-2-3-8-29(28)24-44-32-12-5-4-11-31(32)36-34(41)27-9-6-10-30(21-27)39(42)43/h2-16,21H,17-20,22-24H2,1H3,(H,35,40)(H,36,41)
Release date: 2016-09-21
Notum Fragment 924 (PDB entry 7BDD)
Macromolecule: Palmitoleoyl-protein carboxylesterase NOTUM
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.1.98
Sequence length: 383 residues
Sequence: ETGSAQQLNEDLRLHLLLNTSVTCNDGSPAGYYLKESRGSRRWLLFLEGGWYCFNRENCDSRYDTMRRLMSSRDWPRTRTGTGILSSQPEENPYWWNANMVFIPYCSSDVWSGASSKSEKNEYAFMGALIIQEVVRELLGRGLSGAKVLLLAGSSAGGTGVLLNVDRVAEQLEKLGYPAIQVRGLADSGWFLDNKQYRHTDCVDTITCAPTEAIRRGIRYWNGVVPERCRRQFQEGEEWNCFFGYKVYPTLRSPVFVVQWLFDEAQLTVDNVHLTGQPVQEGLRLYIQNLGRELRHTLKDVPASFAPACLSHEIIIRSHWTDVQVKGTSLPRALHCWDRSLHDSHKASKTPLKGCPVHLVDSCPWPHCNPSCPTGTKHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.47
R work: 0.1985
R free: 0.2106
Average B factor: 22.9907
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 296
Crystal growth procedure: 1.5 M Ammonium Sulphate
0.1 M Sodium Citrate, pH4.2
Matthews coefficient: 1.99
Solvent content (%): 38.29
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: 2022-01-12
Post-catalytic complex of human Polymerase Mu (W434H) mutant with incoming dTTP (PDB entry 5VZI)
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: GSAAASPAWMPAYACQRPTPLTHHNTGLSEALEILAEAAGFEGSEGRLLTFCRAASVLKALPSPVTTLSQLQGLPHFGEHSSRVVQELLEHGVCEEVERVRRSERYQTMKLFTQIFGVGVKTADRWYREGLRTLDDLREQPQKLTQQQKAGLQHHQDLSTPVLRSDVDALQQVVEEAVGQALPGATVTLTGGFRRGKLQGHDVDFLITHPKEGQEAGLLPRVMCRLQDQGLILYHQHQHSCCESPTRLAQQSHMDAFERSFCIFRLPQPGSWKAVRVDLVVAPVSQFPFALLGHTGSKLFQRELRRFSRKEKGLWLNSHGLFDPEQKTFFQAASEEDIFRHLGLEYLPPEQRNA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.5
R work: 0.171
R free: 0.1936
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 95mM HEPES, 19% PEG4K
Matthews coefficient: 2.88
Solvent content (%): 57.4
Ligand: THYMIDINE-5'-TRIPHOSPHATE (TTP)
Ligand formula: C10 H17 N2 O14 P3
Ligand molecular weight: 482.168
Ligand SMILES: CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O
Ligand InChI: InChI=1S/C10H17N2O14P3/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(24-8)4-23-28(19,20)26-29(21,22)25-27(16,17)18/h3,6-8,13H,2,4H2,1H3,(H,19,20)(H,21,22)(H,11,14,15)(H2,16,17,18)/t6-,7+,8+/m0/s1
Release date: 2017-07-05
Aurora A kinase in complex with TPX2-inhibitor 3 (PDB entry 8C15)
Macromolecule: Aurora kinase A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 265 residues
Sequence: MGRQWALEDFEIGRPLGKGKFGNVYLAREKQSKFILALKVLFKAQLEKAGVEHQLRREVEIQSHLRHPNILRLYGYFHDATRVYLILEYAPLGTVYRELQKLSKFDEQRTATYITELANALSYCHSKRVIHRDIKPENLLLGSAGELKIADFGWSVHAPSSRRTTLAGTLDYLPPEMIEGRMHDEKVDLWSLGVLCYEFLVGKPPFEANTYQETYKRISRVEFTFPDFVTEGARDLISRLLKHNPSQRPMLREVLEHPWITANSS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.41
R work: 0.199
R free: 0.207
Average B factor: 75.64
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 6.5
Crystallization temperature (K): 298
Crystal growth procedure: 30% PEG5000 MME, 0.1M (NH4)2SO4, 0.1 M MES 6.5: soaking: 31.5% PEG5000 MME, 0.09M (NH4)2SO4, 0.09 M MES 6.5, 10% DMSO, 5 mM compound
Matthews coefficient: 2.53
Solvent content (%): 51.46
Ligand: ADENOSINE-5'-DIPHOSPHATE (ADP)
Ligand formula: C10 H15 N5 O10 P2
Ligand molecular weight: 427.201
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
Ligand InChI: InChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
Release date: 2024-01-10
Crystal structure of human soluble adenylyl cyclase catalytic domain in complex with the inhibitor TDI-10228 (PDB entry 8COJ)
Macromolecule: Adenylate cyclase type 10
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.6.1.1
Sequence length: 475 residues
Sequence: MNTPKEEFQDWPIVRIAAHLPDLIVYGHFSPERPFMDYFDGVLMFVDISGFTAMTEKFSSAMYMDRGAEQLVEILNYHISAIVEKVLIFGGDILKFAGDALLALWRVERKQLKNIITVVIKCSLEIHGLFETQEWEEGLDIRVKIGLAAGHISMLVFGDETHSHFLVIGQAVDDVRLAQNMAQMNDVILSPNCWQLCDRSMIEIESVPDQRAVKVNFLKPPPNFNFDEFFTKCTTFMHYYPSGEHKNLLRLACTLKPDPELEMSLQKYVMESILKQIDNKQLQGYLSELRPVTIVFVNLMFEDQDKAEEIGPAIQDAYMHITSVLKIFQGQINKVFMFDKGCSFLCVFGFPGEKVPDELTHALECAMDIFDFCSQVHKIQTVSIGVASGIVFCGIVGHTVRHEYTVIGQKVNLAARMMMYYPGIVTCDSVTYNGSNLPAYFFKELPKKVMKGVADSGPLYQYWGRTEKVHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.2008
R free: 0.2254
Average B factor: 53.91
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 277
Crystal growth procedure: 0.2 M tripotassium citrate, 20%(w/v) PEG 3350
Matthews coefficient: 2.6
Solvent content (%): 52.6
Ligand: 4-chloranyl-6-[4-[(3-fluorophenyl)methyl]-1-methyl-pyrazol-3-yl]pyrimidin-2-amine (VE1)
Ligand formula: C15 H13 Cl F N5
Ligand molecular weight: 317.749
Ligand SMILES: Cn1cc(c(n1)c2cc(nc(n2)N)Cl)Cc3cccc(c3)F
Ligand InChI: InChI=1S/C15H13ClFN5/c1-22-8-10(5-9-3-2-4-11(17)6-9)14(21-22)12-7-13(16)20-15(18)19-12/h2-4,6-8H,5H2,1H3,(H2,18,19,20)
Release date: 2023-04-26
Crystal structure of human PDE1B catalytic domain in complex with inhibitor 3 (6-(4-chlorobenzyl)-8,9,10,11-tetrahydrobenzo[4,5]thieno[3,2-e][1,2,4]triazolo[1,5-c]pyrimidin-5(6H)-one) (PDB entry 5UP0)
Macromolecule: Calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.17
Sequence length: 361 residues
Sequence: VGPTYSTAVLNCLKNLDLWCFDVFSLNQAADDHALRTIVFELLTRHNLISRFKIPTVFLMSFLDALETGYGKYKNPYHNQIHAADVTQTVHCFLLRTGMVHCLSEIELLAIIFAAAIHDYEHTGTTNSFHIQTKSECAIVYNDRSVLENHHISSVFRLMQDDEMNIFINLTKDEFVELRALVIEMVLATDMSCHFQQVKTMKTALQQLERIDKPKALSLLLHAADISHPTKQWLVHSRWTKALMEEFFRQGDKEAELGLPFSPLCDRTSTLVAQSQIGFIDFIVEPTFSVLTDVAEKSVQPLADEDSKSKNQPSFQWRQPSLDVEVGDPNPDVVSFRSTWVKRIQENKQKWKERAASGITN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.04
R work: 0.197
R free: 0.2262
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.9
Crystallization temperature (K): 293
Crystal growth procedure: 3.1 M NaCl, 0.1 M HEPES pH 6.9
Matthews coefficient: 3.12
Solvent content (%): 60.55
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: 2017-04-26
ARHGEF2 PanDDA analysis group deposition -- ARHGEF2 and RhoA in complex with Z1545313172 (PDB entry 7G92)
Macromolecule: Transforming protein RhoA
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 185 residues
Sequence: SMAAIRKKLVIVGDGACGKTCLLIVFSKDQFPEVYVPTVFENYVADIEVDGKQVELALWDTAGQEDYDRLRPLSYPDTDVILMCFSIDSPDSLENIPEKWTPEVKHFCPNVPIILVGNKKDLRNDEHTRRELAKMKQEPVKPEEGRDMANRIGAFGYMECSAKTKDGVREVFEMATRAALQARRG
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.872
R work: 0.1979
R free: 0.2374
Average B factor: 32.07
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 100 mM Tris, 2.6M sodium formate
Matthews coefficient: 2.49
Solvent content (%): 50.69
Ligand: DIMETHYL SULFOXIDE (DMS)
Ligand formula: C2 H6 O S
Ligand molecular weight: 78.133
Ligand SMILES: CS(=O)C
Ligand InChI: InChI=1S/C2H6OS/c1-4(2)3/h1-2H3
Release date: 2023-07-12
The crystal structure of human CtsL in complex with 14b (PDB entry 7W34)
Macromolecule: Procathepsin L
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.22.15
Sequence length: 333 residues
Sequence: MNPTLILAAFCLGIASATLTFDHSLEAQWTKWKAMHNRLYGMNEEGWRRAVWEKNMKMIELHNQEYREGKHSFTMAMNAFGDMTSEEFRQVMNGFQNRKPRKGKVFQEPLFYEAPRSVDWREKGYVTPVKNQGQCGSCWAFSATGALEGQMFRKTGRLISLSEQNLVDCSGPQGNEGCNGGLMDYAFQYVQDNGGLDSEESYPYEATEESCKYNPKYSVANDTGFVDIPKQEKALMKAVATVGPISVAIDAGHESFLFYKEGIYFEPDCSSEDMDHGVLVVGYGFESTESDNNKYWLVKNSWGEEWGMGGYVKMAKDRRNHCGIASAASYPTV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.89
R work: 0.2482
R free: 0.3028
Average B factor: 60.9398
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 4.1
Crystallization temperature (K): 289.15
Crystal growth procedure: 100mM sodium acetate (pH 4.1), 15% (w/v) PEG 2000, protein concentration 8mg/ml
Matthews coefficient: 1.83
Solvent content (%): 33.09
Ligand: N-[(2S)-3-cyclohexyl-1-oxidanylidene-1-[[(2S,3S)-3-oxidanyl-4-oxidanylidene-1-[(3S)-2-oxidanylidenepiperidin-3-yl]-4-[(phenylmethyl)amino]butan-2-yl]amino]propan-2-yl]-1-benzofuran-2-carboxamide (89K)
Ligand formula: C34 H42 N4 O6
Ligand molecular weight: 602.72
Ligand SMILES: c1ccc(cc1)CNC(=O)C(C(CC2CCCNC2=O)NC(=O)C(CC3CCCCC3)NC(=O)c4cc5ccccc5o4)O
Ligand InChI: InChI=1S/C34H42N4O6/c39-30(34(43)36-21-23-12-5-2-6-13-23)26(19-25-15-9-17-35-31(25)40)37-32(41)27(18-22-10-3-1-4-11-22)38-33(42)29-20-24-14-7-8-16-28(24)44-29/h2,5-8,12-14,16,20,22,25-27,30,39H,1,3-4,9-11,15,17-19,21H2,(H,35,40)(H,36,43)(H,37,41)(H,38,42)/t25-,26-,27-,30-/m0/s1
Release date: 2023-05-31
Human MRas Q71R in complex with human Shoc2 LRR domain M173I and human PP1Ca (PDB entry 7TXH)
Macromolecule: Ras-related protein M-Ras
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 180 residues
Sequence: GPMATSAVPSDNLPTYKLVVVGDGGVGKSALTIQFFQKIFVPDYDPTIEDSYLKHTEIDNQWAILDVLDTAGREEFSAMREQYMRTGDGFLIVYSVTDKASFEHVDRFHQLILRVKDRESFPMILVANKVDLMHLRKITREQGKEMATKHNIPYIETSAKDPPLNVDKAFHDLVRVIRQQ
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.95
R work: 0.1671
R free: 0.2103
Average B factor: 36.29
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M NaH2PO4 pH 6.5, 12% PEG 8000
Matthews coefficient: 2.6
Solvent content (%): 52.73
Ligand: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER (GNP)
Ligand formula: C10 H17 N6 O13 P3
Ligand molecular weight: 522.196
Ligand SMILES: c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N=C(NC2=O)N
Ligand InChI: InChI=1S/C10H17N6O13P3/c11-10-13-7-4(8(19)14-10)12-2-16(7)9-6(18)5(17)3(28-9)1-27-32(25,26)29-31(23,24)15-30(20,21)22/h2-3,5-6,9,17-18H,1H2,(H,25,26)(H3,11,13,14,19)(H4,15,20,21,22,23,24)/t3-,5-,6-,9-/m1/s1
Release date: 2022-06-22
Nucleotide-free Mitofusin2 (MFN2) (PDB entry 6JFL)
Macromolecule: Mitofusin-2,cDNA FLJ57997, highly similar to Transmembrane GTPase MFN2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5
Sequence length: 438 residues
Sequence: GPHMGGSAEVNASPLKHFVTAKKKINGIFEQLGAYIQESATFLEDTYRNAELDPVTTEEQVLDVKGYLSKVRGISEVLARRHMKVAFFGRTSNGKSTVINAMLWDKVLPSGIGHTTNCFLRVEGTDGHEAFLLTEGSEEKRSAKTVNQLAHALHQDKQLHAGSLVSVMWPNSKCPLLKDDLVLMDSPGIDVTTELDSWIDKFCLDADVFVLVANSESTLMQTEKHFFHKVSERLSRPNIFILNNRWDASASEPEYMEEVRRQHMERCTSFLVDELGVVDRSQAGDRIFFVSAKEVLNARIQKAQGMPEGGGALAEGFQVRMFEFQNFERRFEECISQSAVKTKFEQHTVRAKQIAEAVRLIMDSLHMAAREQQVYCEEMREERQDRTRENLEQEIAAMNKKIEVLDSLQSKAKLLRNKAGWLDSELNMFTHQYLQPSR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.806
R work: 0.207
R free: 0.2832
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293.15
Crystal growth procedure: 0.19 M Calcium chloride
0.095 M HEPES PH7.5
26.6% (V/V) PEG400
5% (V/V) Glycerol
Matthews coefficient: 2.39
Solvent content (%): 48.43
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: 2019-11-13
The crystal structure of the GST-like domains complex of EPRS-AIMP2 (PDB entry 5A34)
Macromolecule: BIFUNCTIONAL GLUTAMATE/PROLINE--TRNA LIGASE
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.1.1.15
Sequence length: 175 residues
Sequence: MATLSLTVNSGDPPLGALLAVEHVKDDVSISVEEGKENILHVSENVIFTDVNSILRYLARVATTAGLYGSNLMEHTEIDHWLEFSATKLSSCDSFTSTINELNHCLSLRTYLVGNSLSLADLCVWATLKGNAAWQEQLKQKKAPVHVKRWFGFLEAQQAFQSVGTKWDVSTTKAR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.6
R work: 0.1886
R free: 0.2473
Crystallization pH: 7.5
Crystal growth procedure: PEG 3350 22% , 0.2 M AMMONIUM CHLORIDE, pH 7.5
Matthews coefficient: 2.61
Solvent content (%): 52.83
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: 2015-10-21
Thrombin in complex with D-Phe-Pro-3-chloro-1,3-dihydroxybenzylamide derivative (13c) (PDB entry 6YB6)
Macromolecule: Prothrombin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.5
Sequence length: 36 residues
Sequence: TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.33
R work: 0.1309
R free: 0.1526
Average B factor: 22.9854
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 20mM sodium dihydrogen phosphate ph 7.5
350mM NaCl
27% PEG 8000
Matthews coefficient: 2.84
Solvent content (%): 56.77
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2021-03-31
Crystal structure of bat influenza A/H17N10 polymerase with viral RNA promoter bound to a 19-mer serine 5 phosphorylated Pol II CTD peptide with a truncated linker. (PDB entry 6FHI)
Macromolecule: Polymerase acidic protein
Type: Protein, polypeptide(L)
Source organism: Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10))
Sequence length: 738 residues
Sequence: GSHHHHHHHHGSGSMENFVRTNFNPMILERAEKTMKEYGENPQNEGNKFAAISTHMEVCFMYSDFHFIDLEGNTIVKENDDDNAMLKHRFEIIEGQERNIAWTIVNSICNMTENSKPRFLPDLYDYKTNKFIEIGVTRRKVEDYYYEKASKLKGENVYIHIFSFDGEEMATDDEYILDEESRARIKTRLFVLRQELATAGLWDSFRQSEKGEETLEEEFSYPPTFQRLANQSLPPSFKDYHQFKAYVSSFKANGNIEAKLGAMSEKVNAQIESFDPRTIRELELPEGKFCTQRSKFLLMDAMKLSVLNPAHEGEGIPMKDAKACLDTFWGWKKATIIKKHEKGVNTNYLMIWEQLLESIKEMEGKFLNLKKTNHLKWGLGEGQAPEKMDFEDCKEVPDLFQYKSEPPEKRKLASWIQSEFNKASELTNSNWIEFDELGNDVAPIEHIASRRRNFFTAEVSQCRASEYIMKAVYINTALLNSSCTAMEEYQVIPIITKCRDTSGQRRTNLYGFIIKGRSHLRNDTDVVNFISLEFSLTDPRNEIHKWEKYCVLEIGDMEIRTSISTIMKPVYLYVRTNGTSKIKMKWGMEMRRCLLQSLQQVESMIEAESAVKEKDMTEPFFRNRENDWPIGESPQGIEKGTIGKVCRVLLAKSVFNSIYASAQLEGFSAESRKLLLLIQAFRDNLDPGTFDLKGLYEAIEECIINDPWVLLNASWFNSFLKAVQLSMGSGSGENLYFQ
Oligomeric state: Hetero 4-mer
Stoichiometry: A1, B1, C1, D1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.8
R work: 0.23016
R free: 0.26978
Average B factor: 81.201
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5
Crystallization temperature (K): 277
Crystal growth procedure: Bat FluA polymerase bound to the ends of the RNA promotor (5 prime end nts 1-16, 3 prime end nts 1-18) was co-crystallized in a 1:8 ratio with the  serine 5 phosphorylated  19-mer Pol II CTD peptide mimic, with a truncated linker, in 0.8 M sodium-potassium phosphate at pH 5.0. Crystals were set at 4 C using seeding.
Matthews coefficient: 3.33
Solvent content (%): 63.05
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: 2019-01-30
Crystal structure of EGFR_TMX in complex with covalently bound fragment 8 (PDB entry 8HV6)
Macromolecule: Epidermal growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 331 residues
Sequence: GSGEAPNQALLRILKETEFKKIKVLGSGAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMASVDNPHVCRLLGICLTSTVQLIMQLMPFGSLLDYVREHKDNIGSQYLLNWCVQIAKGMNYLEDRRLVHRDLAARNVLVKTPQHVKITDFGRAKLLGAAAAEYHAEGGKVPIKWMALESILHRIYTHQSDVWSYGVTVWELMTFGSKPYDGIPASEISSILEKGERLPQPPICTIDVYMIMVKCWMIDADSRPKFRELIIEFSKMARDPQRYLVIQGDERMHLPSPTDSNFYRALMDEEDMDDVVDADEYLIPQQGNS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.24702
R free: 0.29574
Average B factor: 36.427
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 292
Crystal growth procedure: 0.1M TRIS pH 8.5, 0.15M Sodium citrate, 25%PEG400
Matthews coefficient: 3.3
Solvent content (%): 62.75
Ligand: 3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL (PE5)
Ligand formula: C18 H38 O9
Ligand molecular weight: 398.489
Ligand SMILES: CCOCCOCCOCCOCCOCCOCCOCCOCCO
Ligand InChI: InChI=1S/C18H38O9/c1-2-20-5-6-22-9-10-24-13-14-26-17-18-27-16-15-25-12-11-23-8-7-21-4-3-19/h19H,2-18H2,1H3
Release date: 2023-12-13
CRYSTAL STRUCTURE OF HUMAN INDOLEAMINE 2,3-DIOXYGENASE 1 (IDO1) free enzyme in the ferric state (PDB entry 6E44)
Macromolecule: Indoleamine 2,3-dioxygenase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.13.11.52
Sequence length: 405 residues
Sequence: MGSSHHHHHHSSGSAAYHIDEEVGFALPNPQENLPDFYNDWMFIAKHLPDLIESGQLRERVEKLNMLSIDHLTDHKSQRLARLVLGCITMAYVWGKGHGDVRKVLPRNIAVPYCQLSAALELPPILVYADCVLANWKKKDPNKPLTYENMDVLFSFRDGDCSKGFFLVSLLVEIAAASAIKVIPTVFKAMQMQERDTLLKALLEIASCLEKALQVFHQIHDHVNPKAFFSVLRIYLSGWKGNPQLSDGLVYEGFWEDPKEFAGGSAGQSSVFQCFDVLLGIQQTAGGGHAAQFLQDMRRYMPPAHRNFLCSLESNPSVREFVLSKGDAGLREAYDACVKALVSLRSYHLQIVTKYILIPASQQPKENKTSEDPSKLEAKGTGGTDLMNFLKTVRSTTEKSLLKEG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.903
R work: 0.1941
R free: 0.2347
Average B factor: 35.3009
Crystallization method: EVAPORATION
Crystallization pH: 6.2
Crystallization temperature (K): 298
Crystal growth procedure: 0.1 M phosphate (pH 6.2), and 15% (w/v) PEG3350
Matthews coefficient: 2.51
Solvent content (%): 51.04
Ligand: PROTOPORPHYRIN IX CONTAINING FE (HEM)
Ligand formula: C34 H32 Fe N4 O4
Ligand molecular weight: 616.487
Ligand SMILES: Cc1c2n3c(c1CCC(=O)O)C=C4C(=C(C5=[N]4[Fe]36[N]7=C(C=C8N6C(=C5)C(=C8C)C=C)C(=C(C7=C2)C)C=C)C)CCC(=O)O
Ligand InChI: InChI=1S/C34H34N4O4.Fe/c1-7-21-17(3)25-13-26-19(5)23(9-11-33(39)40)31(37-26)16-32-24(10-12-34(41)42)20(6)28(38-32)15-30-22(8-2)18(4)27(36-30)14-29(21)35-25;/h7-8,13-16H,1-2,9-12H2,3-6H3,(H4,35,36,37,38,39,40,41,42);/q;+2/p-2/b25-13-,26-13-,27-14-,28-15-,29-14-,30-15-,31-16-,32-16-;
Release date: 2018-11-14
Crystal Structure of Human DNA Polymerase Eta Inserting dGMPNPP Opposite O4-Methylhymidine (PDB entry 5DLG)
Macromolecule: DNA polymerase eta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 435 residues
Sequence: GPHMATGQDRVVALVDMDCFFVQVEQRQNPHLRNKPCAVVQYKSWKGGGIIAVSYEARAFGVTRSMWADDAKKLCPDLLLAQVRESRGKANLTKYREASVEVMEIMSRFAVIERASIDEAYVDLTSAVQERLQKLQGQPISADLLPSTYIEGLPQGPTTAEETVQKEGMRKQGLFQWLDSLQIDNLTSPDLQLTVGAVIVEEMRAAIERETGFQCSAGISHNKVLAKLACGLNKPNRQTLVSHGSVPQLFSQMPIRKIRSLGGKLGASVIEILGIEYMGELTQFTESQLQSHFGEKNGSWLYAMCRGIEHDPVKPRQLPKTIGCSKNFPGKTALATREQVQWWLLQLAQELEERLTKDRNDNDRVATQLVVSIRVQGDKRLSSLRRCCALTRYDAHKMSHDAFTVIKNCNTSGIQTEWSPPLTMLFLCATKFSAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.351
R work: 0.1718
R free: 0.2475
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 291
Crystal growth procedure: 0.1 M MES pH 5.5, 5mM magnesium chloride, 20% PEG 2000 MME
Matthews coefficient: 2.11
Solvent content (%): 41.69
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: 2016-08-10