satarupa22/MacromolecularLigandDB huggingface dataset:
Evolutionary gain of alanine mischarging to non-cognate tRNAs with a G4:U69 base pair (PDB entry 5KNN)
Macromolecule: Alanine--tRNA ligase, cytoplasmic
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.1.1.7
Sequence length: 450 residues
Sequence: TLTASEIRQRFIDFFKRNEHTYVHSSATIPLDDPTLLFANAGMNQFKPIFLNTIDPSHPMAKLSRAANTQKCIRAGGKHNDLDDVGKDVYHHTFFEMLGSWSFGDYFKELACKMALELLTQEFGIPIERLYVTYFGGDEAAGLEADLECKQIWQNLGLDDTKILPGNMKDNFWEMGDTGPCGPCSEIHYDRIGGRDAAHLVNQDDPNVLEIWNLVFIQYNREADGILKPLPKKSIDTGMGLERLVSVLQNKMSNYDTDLFVPYFEAIQKGTGARPYTGKVGAEDADGIDMAYRVLADHARTITVALADGGRPDNTGRGYVLRRILRRAVRYAHEKLNASRGFFATLVDVVVQSLGDAFPELKKDPDMVKDIINEEEVQFLKTLSRGRRILDRKIQSLGDSKTIPGDTAWLLYDTYGFPVDLTGLIAEEKGLVVDMDGFEEERKLAQLKSQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.68
R work: 0.216
R free: 0.2542
Average B factor: 55.755
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 289
Crystal growth procedure: 0.1 M Hepes pH 7.5, 20% Polyethylene glycol 3350, 0.2 M MgCl2
Matthews coefficient: 2.55
Solvent content (%): 51.74
Ligand: '5'-O-(N-(L-ALANYL)-SULFAMOYL)ADENOSINE (A5A)
Ligand formula: C13 H19 N7 O7 S
Ligand molecular weight: 417.398
Ligand SMILES: CC(C(=O)NS(=O)(=O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)O)N
Ligand InChI: InChI=1S/C13H19N7O7S/c1-5(14)12(23)19-28(24,25)26-2-6-8(21)9(22)13(27-6)20-4-18-7-10(15)16-3-17-11(7)20/h3-6,8-9,13,21-22H,2,14H2,1H3,(H,19,23)(H2,15,16,17)/t5-,6+,8+,9+,13+/m0/s1
Release date: 2016-09-28
Crystal Structure of a human Lysosome Resident Glycoprotein, Lysosomal Acid Lipase, and its Implications in Cholesteryl Ester Storage Disease (CESD) (PDB entry 6V7N)
Macromolecule: Lysosomal acid lipase/cholesteryl ester hydrolase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.1.13
Sequence length: 384 residues
Sequence: SGGKLTAVDPETNMNVSEIISYWGFPSEEYLVETEDGYILCLNRIPHGRKQHSDKGPKPVVFLQHGLLADSSNWVTNLAQSSLGFILADAGFDVWMGNSRGNTWSRKHKTLSVSQDEFWAFSYDEMAKYDLPASINFILNKTGQEQVYYVGHSQGTTIGFIAFSQIPELAKRIKMFFALGPVASVAFCTSPMAKLGRLPDHLIKDLFGDKEFLPQSAFLKWLGTHVCTHVILKELCGNLCFLLCGFNERNLNMSRVDVYTTHSPAGTSVQNMLHWSQAVKFQKFQAFDWGSSAKNYFHYQQSYPPTYNVKDMLVPTAVWSGGHDWLADVYDVNILLTQITNLVFHESIPEWEHLDFIWGLDAPWRLYNKIINLMRKYQASENNL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.62
R work: 0.185
R free: 0.222
Average B factor: 58.59
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 1.8 M Ammonium sulfate, 0.1 M CH3COONa, pH 5.5
Matthews coefficient: 2.77
Solvent content (%): 55.67
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: 2020-06-17
Crystal Structure of a Variant Human Activation-induced Deoxycytidine Deaminase as an MBP fusion protein (PDB entry 5JJ4)
Macromolecule: Maltose-binding periplasmic protein,Single-stranded DNA cytosine deaminase
Type: Protein, polypeptide(L)
Source organism: Escherichia coli O157:H7
EC number: 3.5.4.38
Sequence length: 546 residues
Sequence: KIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDAALAAAQTNAAALMDPHIFTSNFNNGIGRHKTYLCYEVERLDSATSFSLDFGYLRNKNGCHVELLFLRYISDWDLDPGRCYRVTWFTSWSPCYDCARHVADFLRGNPNLSLRIFTARLYFCEDRKAEPEGLRRLHRAGVQIAIMTFKDYFYCWNTFVENHERTFKAWEGLHENSVRLSRQLRRILLPL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.807
R work: 0.1831
R free: 0.2318
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 100mM MES pH 6.5, 200mM Calcium Acetate, 15%PEG8000
Matthews coefficient: 2.97
Solvent content (%): 58.59
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: 2016-06-29