satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of cysteine-bound ferrous form of the uncrosslinked F2-Tyr157 human cysteine dioxygenase (PDB entry 6BPS)
Macromolecule: Cysteine dioxygenase type 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.13.11.20
Sequence length: 200 residues
Sequence: SEQTEVLKPRTLADLIRILHQLFAGDEVNVEEVQAIMEAYESDPTEWAMYAKFDQYRYTRNLVDQGNGKFNLMILCWGEGHGSSIHDHTNSHCFLKMLQGNLKETLFAWPDKKSNEMVKKSERVLRENQCAYINDSVGLHRVENISHTEPAVSLHLXSPPFDTCHAFDQRTGHKNKVTMTFHSKFGIRTPNATSGSLENN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.1668
R free: 0.2031
Average B factor: 28.4391
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 295
Crystal growth procedure: 0.1 M MES, 2 M ammonium sulfate, 2% PEG400
Matthews coefficient: 3.69
Solvent content (%): 66.68
Ligand: FE (II) ION (FE2)
Ligand formula: Fe
Ligand molecular weight: 55.845
Ligand SMILES: [Fe+2]
Ligand InChI: InChI=1S/Fe/q+2
Release date: 2018-07-04
Human LanCL1 C264A mutant bound to GSH (PDB entry 8D0V)
Macromolecule: Glutathione S-transferase LANCL1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.5.1.18
Sequence length: 419 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMAQRAFPNPYADYNKSLAEGYFDAAGRLTPEFSQRLTNKIRELLQQMERGLKSADPRDGTGYTGWAGIAVLYLHLYDVFGDPAYLQLAHGYVKQSLNCLTKRSITFLCGDAGPLAVAAVLYHKMNNEKQAEDCITRLIHLNKIDPHAPNEMLYGRIGYIYALLFVNKNFGVEKIPQSHIQQICETILTSGENLARKRNFTAKSPLMYEWYQEYYVGAAHGLAGIYYYLMQPSLQVSQGKLHSLVKPSVDYVCQLKFPSGNYPPAIGDNRDLLVHWCHGAPGVIYMLIQAYKVFREEKYLCDAYQCADVIWQYGLLKKGYGLCHGSAGNAYAFLTLYNLTQDMKYLYRACKFAEWCLEYGEHGCRTPDTPFSLFEGMAGTIYFLADLLVPTKARFPAFEL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.79
R work: 0.18145
R free: 0.20186
Average B factor: 29.95
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 282.15
Crystal growth procedure: 0.70-0.75 M succinic acid pH 7.0, 0.1 M bis-tris-propane pH 7.0.
Matthews coefficient: 2.63
Solvent content (%): 53.23
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: 2023-01-25
Crystal structure of human Pim-1 kinase in complex with a consensus peptide and fragment like molecule 2,5-dihydro-1H-isothiochromeno[3,4-d]pyrazol-3-one (PDB entry 5N4Y)
Macromolecule: Serine/threonine-protein kinase pim-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 313 residues
Sequence: MLLSKINSLAHLRAAPCNDLHATKLAPGKEKEPLESQYQVGPLLGSGGFGSVYSGIRVSDNLPVAIKHVEKDRISDWGELPNGTRVPMEVVLLKKVSSGFSGVIRLLDWFERPDSFVLILERPEPVQDLFDFITERGALQEELARSFFWQVLEAVRHCHNCGVLHRDIKDENILIDLNRGELKLIDFGSGALLKDTVYTDFDGTRVYSPPEWIRYHRYHGRSAAVWSLGILLYDMVCGDIPFEHDEEIIGGQVFFRQRVSSECQHLIRWCLALRPSDRPTFEEIQNHPWMQDVLLPQETAEIHLHSLSPGPSK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.56
R work: 0.1744
R free: 0.2177
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 277
Crystal growth procedure: HEPES
LiCl
Glycerol
DTT
BIS-TRIS-propane
PEG3350
Ethylene-glycol
DMSO
Matthews coefficient: 3.15
Solvent content (%): 61
Ligand: 2,5-dihydro-1~{H}-isothiochromeno[4,3-c]pyrazol-3-one (8N5)
Ligand formula: C10 H8 N2 O S
Ligand molecular weight: 204.248
Ligand SMILES: c1ccc2c(c1)CSC3=C2NNC3=O
Ligand InChI: InChI=1S/C10H8N2OS/c13-10-9-8(11-12-10)7-4-2-1-3-6(7)5-14-9/h1-4H,5H2,(H2,11,12,13)
Release date: 2018-02-28
apo-Carbonic Anhydrase II soaked in 3NPA after UV at 120 K (PDB entry 7Y2L)
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): 1.25
R work: 0.11979
R free: 0.16385
Average B factor: 14.75
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 (%): 40.89
Release date: 2023-12-20
ERK2 complexed with N-benzylpyridone tetrahydroazaindazole (PDB entry 5BUE)
Macromolecule: Mitogen-activated protein kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.24
Sequence length: 361 residues
Sequence: GPAAAAAAGAGPEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFEHQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKLLKTQHLSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLLNTTCDLKICDFGLARVADPDHDHTGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILGILGSPSQEDLNCIINLKARNYLLSLPHKNKVPWNRLFPNADSKALDLLDKMLTFNPHKRIEVEQALAHPYLEQYYDPSDEPIAEAPFKFDMELDDLPKEKLKELIFEETARFQPGYRS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.4
R work: 0.1824
R free: 0.2299
Average B factor: 34.68
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291
Crystal growth procedure: RESERVOIR SOLUTION : 0.2M MAGNESIUM FORMATE, 20% PEG 3350 
          
PROTEIN SOLUTION   : 20.7MG/ML IN 20MM TRIS PH 7.5, 150MM NACL, 1MM TCEP(NO GLYCEROL)                          

SOAKING PROTOCOL: COMPOUND WAS INCUBATED WITH THE PROTEIN AT 1MM FINAL CONCENTRATION BEFORE SETUP.  EQUAL VOLUMES OF PROTEIN AND CRYSTALLANT WERE ADDED TO COVERSLIP            

CRYO PROTOCOL : SOAKING BUFFER: 0.2M MAGNESIUM FORMATE, 20% PEG 3350, 20% GLYCEROL, 2MM COMPOUND A CRYSTAL WAS TRANSFERRED TO A 5UL SOAKING BUFFER ON A SCREWED CUP LID. 100UL  OF RESERVOIR VOLUME WAS USED TO KEEP THE DROP FROM DRYING-OUT
Matthews coefficient: 2.26
Solvent content (%): 45.47
Ligand: NICKEL (II) ION (NI)
Ligand formula: Ni
Ligand molecular weight: 58.693
Ligand SMILES: [Ni+2]
Ligand InChI: InChI=1S/Ni/q+2
Release date: 2015-07-15
AKR1C3 complexed with new inhibitor with novel scaffold (PDB entry 6A7B)
Macromolecule: Aldo-keto reductase family 1 member C3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1
Sequence length: 323 residues
Sequence: MDSKHQCVKLNDGHFMPVLGFGTYAPPEVPRSKALEVTKLAIEAGFRHIDSAHLYNNEEQVGLAIRSKIADGSVKREDIFYTSKLWSTFHRPELVRPALENSLKKAQLDYVDLYLIHSPMSLKPGEELSPTDENGKVIFDIVDLCTTWEAMEKCKDAGLAKSIGVSNFNRRQLEMILNKPGLKYKPVCNQVECHPYFNRSKLLDFCKSKDIVLVAYSALGSQRDKRWVDPNSPVLLEDPVLCALAKKHKRTPALIALRYQLQRGVVVLAKSYNEQRIRQNVQVFEFQLTAEDMKAIDGLDRNLHYFNSDSFASHPNYPYSDEY
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.37
R work: 0.1635
R free: 0.2311
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 289
Crystal growth procedure: 15-20% (w/v) PEG 8000, 100 mM MES, 0.14M NaCl
Matthews coefficient: 2.1
Solvent content (%): 41.54
Ligand: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE (NAP)
Ligand formula: C21 H28 N7 O17 P3
Ligand molecular weight: 743.405
Ligand SMILES: c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)OP(=O)(O)O)O)O)O)C(=O)N
Ligand InChI: InChI=1S/C21H28N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1-4,7-8,10-11,13-16,20-21,29-31H,5-6H2,(H7-,22,23,24,25,32,33,34,35,36,37,38,39)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
Release date: 2019-07-03
CRYSTAL STRUCTURE OF AN ACTIVE KRAS G12D (GPPCP) DIMER IN COMPLEX WITH BI-5747 (PDB entry 7ACA)
Macromolecule: GTPase KRas
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 170 residues
Sequence: GMTEYKLVVVGADGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEK
Oligomeric state: Homo 2-mer
Stoichiometry: A2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.57
R work: 0.189
R free: 0.205
Average B factor: 28.63
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 294
Crystal growth procedure: Morpheus Screen D12

Morpheus Alcohol 10%
Morpheus Buffer 3
MPD_P1K_P3350 37.5% w/v
Matthews coefficient: 2.16
Solvent content (%): 43.15
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: 2020-11-18
KRAS4b K117N 1-185 bound to GNP-Mg2+ (PDB entry 8EIE)
Macromolecule: GTPase KRas
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 185 residues
Sequence: MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNNCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEKMSKDGKKKKKKSKTKS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.41
R work: 0.1817
R free: 0.205
Average B factor: 26.05
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293.15
Crystal growth procedure: 30% PEG4000, 0.2 M sodium acetate, 0.1 M Tris-HCl pH 8.5, 20 mM sodium chloride, 1 mM magnesium chloride, 2 mM DTT, 2 mM GNP, 15 mg/ml KRAS K117N
Matthews coefficient: 2.23
Solvent content (%): 44.74
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: 2023-09-20
Human DNMT3B PWWP domain in complex with N,N-bis(2-hydroxypropyl)ethanolamine (PDB entry 5NRS)
Macromolecule: DNA (cytosine-5)-methyltransferase 3B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.37
Sequence length: 150 residues
Sequence: EADSGDGDSSEYQDGKEFGIGDLVWGKIKGFSWWPAMVVSWKATSKRQAMSGMRWVQWFGDGKFSEVSADKLVALGLFSQHFNLATFNKLVSYRKAMYHALEKARVRAGKTFPSSPGDSLEDQLKPMLEWAHGGFKPTGIEGLKPNNTQP
Oligomeric state: Homo 2-mer
Stoichiometry: A2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.1951
R free: 0.2477
Average B factor: 60.46
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 0.1 M MES,0.2 M Li2SO4, 23-33% PEG 3350
Matthews coefficient: 3.82
Solvent content (%): 67.81
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: 2018-05-30
Crystal structure of the S23226G missense variant of titin domain Fn3-56 (PDB entry 8ORL)
Macromolecule: Titin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 105 residues
Sequence: GSSGPPGPPEKPEVSNVTKNTATVSWKRPVDDGGSEITGYHVERREKKSLRWVRAIKTPVSDLRCKVTGLQEGSTYEFRVSAENRAGIGPPGEASDSVLMKDAAY
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.43
R work: 0.1587
R free: 0.1941
Average B factor: 20.88
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 10mM Tris-HCl pH 7.5
50mM NaCl
0.5mM DTT
0.1M MES
10mM ZnCl2
20% (w/v) PEG6000
Matthews coefficient: 2.28
Solvent content (%): 46.1
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: 2023-08-23
Crystal structure of human Naa60 in complex with acetyl-CoA (PDB entry 5HGZ)
Macromolecule: N-alpha-acetyltransferase 60
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 243 residues
Sequence: SMTEEERSSALSEVSLRLLCHDDIDTVKHLCGDWFPIEYPDSWYRDITSNKKFFSLAATYRGAIVGMIVAEIKNRTKIHKEDGDILASNFSVDTQVAYILSLGVVKEFRKHGIGSLLLESLKDHISTTAQDHCKAIYLHVLTTNNTAINFYENRDFKQHHYLPYYYSIRGVLKDGFTYVLYINGGHPPWTILDYIQHLGSALASLSPCSIPHRVYRQAHSLLCSFLPWSGISSKSGIEYSRTM
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.383
R work: 0.1824
R free: 0.1918
Crystallization method: LIQUID DIFFUSION
Crystallization pH: 4
Crystallization temperature (K): 293.15
Crystal growth procedure: 10mM Tris pH 8.0, 75mM NaCl, 0.5% glycerol, 3%(v/v) Tacsimate pH4.0 (Hampton Research) and 7.5%(w/v) polyethylene glycol 3350 (PEG 3350)
Matthews coefficient: 1.9
Solvent content (%): 35.23
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: 2016-09-14
Human Aldose Reductase complexed with a ligand with an IDD structure (2-[2-(1,3-benzothiazol-2-ylmethylcarbamoyl)-5-fluoro-phenoxy]acetic acid) at 1.05 A (PDB entry 4QR6)
Macromolecule: Aldose reductase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.1.1.21
Sequence length: 316 residues
Sequence: MASRILLNNGAKMPILGLGTWKSPPGQVTEAVKVAIDVGYRHIDCAHVYQNENEVGVAIQEKLREQVVKREELFIVSKLWCTYHEKGLVKGACQKTLSDLKLDYLDLYLIHWPTGFKPGKEFFPLDESGNVVPSDTNILDTWAAMEELVDEGLVKAIGISNFNHLQVEMILNKPGLKYKPAVNQIECHPYLTQEKLIQYCQSKGIVVTAYSPLGSPDRPWAKPEDPSLLEDPRIKAIAAKHNKTTAQVLIRFPMQRNLVVIPKSVTPERIAENFKVFDFELSSQDMTTLLSYNRNWRVCALLSCTSHKDYPFHEEF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.05
R work: 0.1405
R free: 0.1569
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 291
Crystal growth procedure: Crystallization solution: 50 mM di-Ammoniumhydrogen citrate pH 5.0 PEG6000= 5 % (m/V) DTT= 5.15 g/L NADP+= 0.66 g/L and Human Aldose Reductase= 15 mg/ml.Afterwards the crystals were soaked into Tris 100 mM 25% (m/V) PEG6000 pH 8.0 saturated with the inhibitor.The well solution was for crystallization was 120mM di-Ammonium hydrogen citrate with 20% PEG6000 pH 5.0., VAPOR DIFFUSION, HANGING DROP, temperature 291K
Matthews coefficient: 2.18
Solvent content (%): 43.46
Ligand: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE (NAP)
Ligand formula: C21 H28 N7 O17 P3
Ligand molecular weight: 743.405
Ligand SMILES: c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)OP(=O)(O)O)O)O)O)C(=O)N
Ligand InChI: InChI=1S/C21H28N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1-4,7-8,10-11,13-16,20-21,29-31H,5-6H2,(H7-,22,23,24,25,32,33,34,35,36,37,38,39)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
Release date: 2015-08-12
Crystal structure of human PLK1 Polo-Box Domain in complex with Mis18 (PDB entry 8S30)
Macromolecule: Serine/threonine-protein kinase PLK1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.21
Sequence length: 242 residues
Sequence: RSMETGEVVDCHLSDMLQQLHSVNASKPSERGLVRQEEAEDPACIPIFWVSKWVDYSDKYGLGYQLCDNSVGVLFNDSTRLILYNDGDSLQYIERDGTESYLTVSSHPNSLMKKITLLKYFRNYMSEHLLKAGANITPREGDELARLPYLRTWFRTRSAIILHLSNGSVQINFFQDHTKLILCPLMAAVTYIDEKRDFRTYRLSLLEEYGCCKELASRLRYARTMVDKLLSSRSASNRLKAS
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.94
R work: 0.2169
R free: 0.2707
Average B factor: 35.5
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 0.09 M Halogen mix (NaF, NaBr, NaI), 0.1 M buffer
system 2 (Sodium HEPES and MOPS) (pH7.5), 37% precipitant mix
MPD_P1K_P3350 (MPD (racemic), PEG 1K, PEG 3350)
Matthews coefficient: 1.89
Solvent content (%): 35.08
Release date: 2024-08-21
Zn-Carbonic Anhydrase II complexed with 3NPA after UV at 180 K (PDB entry 7Y2H)
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: 0.12026
R free: 0.14926
Average B factor: 16.298
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: 2.1
Solvent content (%): 41.32
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: 2023-12-20
Crystal structure of human protein kinase CK2alpha' (CSNK2A2 gene product) in complex with the ATP-competitive inhibitor 6-bromo-5-chloro-1H-triazolo[4,5-b]pyridine (PDB entry 7A1Z)
Macromolecule: Casein kinase II subunit alpha'
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 364 residues
Sequence: MGSSHHHHHHSQDPMPGPAAGSRARVYAEVNSLRSREYWDYEAHVPSWGNQDDYQLVRKLGRGKYSEVFEAINITNNERVVVKILKPVKKKKIKREVKILENLRGGTNIIKLIDTVKDPVSKTPALVFEYINNTDFKQLYQILTDFDIRFYMYELLKALDYCHSKGIMHRDVKPHNVMIDHQQKKLRLIDWGLAEFYHPAQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRREPFFHGQDNYDQLVRIAKVLGTEELYGYLKKYHIDLDPHFNDILGQHSRKRWENFIHSENRHLVSPEALDLLDKLLRYDHQQRLTAKEAMEHPYFYPVVKEQSQPSADNAVLSSGLTAAR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.024
R work: 0.1347
R free: 0.1468
Average B factor: 17.21
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: Reservoir composition: 28 % (w/v) PEG6000, 0.9 M LiCl, 0.1 M, Tris/HCl, pH 8.5; drop composition prior to equilibration: 0.01 ml reservoir solution + 0.02 ml CK2alpha' (mutant Cys336Ser)/inhibitor MB002 mixture (0.180 ml 6 mg/ml CK2alpha'Cys336Ser, 0.5 M NaCl, 25 mM Tris/HCl, pH 8.5, mixed and pre-equilibrated with 0.02 ml 10 mM MB002 in dimethyl sulfoxide); the initial inhibitor MB002 was replaced by the inhibitor 6-bromo-5-chloro-1H-triazolo[4,5-b]pyridine by extensive crystal soaking.
Matthews coefficient: 2.62
Solvent content (%): 53.06
Ligand: 6-bromanyl-5-chloranyl-1~{H}-[1,2,3]triazolo[4,5-b]pyridine (QWN)
Ligand formula: C5 H2 Br Cl N4
Ligand molecular weight: 233.453
Ligand SMILES: c1c2c(nc(c1Br)Cl)nn[nH]2
Ligand InChI: InChI=1S/C5H2BrClN4/c6-2-1-3-5(8-4(2)7)10-11-9-3/h1H,(H,8,9,10,11)
Release date: 2020-12-09
Thrombin in Complex with a D-Phe-Pro-2-aminopyridine derivative (PDB entry 6T3Q)
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: 0.1252
R free: 0.1458
Average B factor: 18.58
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 20 mM NaH2PO4 (pH 7.5), 350 mM NaCl, 27% (w/v) PEG8000
Matthews coefficient: 2.5
Solvent content (%): 50.87
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: 2020-05-13
Crystal Structure of human phosphodiesterase 10 in complex with 3-N-[2-(4-fluorophenyl)imidazo[1,2-a]pyridin-7-yl]-4-N,4-N,2-trimethylpyrazole-3,4-dicarboxamide (PDB entry 5SGM)
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): 2.2
R work: 0.1903
R free: 0.231
Average B factor: 38.676
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: 2.99
Solvent content (%): 58.9
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: 2022-10-12
Crystal structure of SIRT3 in complex with H4K16la peptide (PDB entry 8HLW)
Macromolecule: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.286
Sequence length: 281 residues
Sequence: DKGKLSLQDVAELIRARACQRVVVMVGAGISTPSGIPDFRSPGSGLYSNLQQYDLPYPEAIFELPFFFHNPKPFFTLAKELYPGNYKPNVTHYFLRLLHDKGLLLRLYTQNIDGLERVSGIPASKLVEAHGTFASATCTVCQRPFPGEDIRADVMADRVPRCPVCTGVVKPDIVFFGEPLPQRFLLHVVDFPMADLLLILGTSLEVEPFASLTEAVRSSVPRLLINRDLVGPLAWHPRSRDVAQLGDVVHGVESLVELLGWTEEMRDLVQRETGKLDGPDK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.1878
R free: 0.2431
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 289
Crystal growth procedure: 0.1 M Tris pH 8.5, 25% (w/v) Polyethylene glycol 3350
Matthews coefficient: 2.56
Solvent content (%): 51.88
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: 2023-09-27