satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of carbonic anhydrase 2 with 4-(2-chlorophenyl)-3a,4,5,9b-tetrahydro-3H-cyclopenta[c]quinoline-8-sulfonamide (PDB entry 6SX9)
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): 1.43
R work: 0.1505
R free: 0.1786
Average B factor: 15.032
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 296
Crystal growth procedure: 1.5 M sodium citrate, 0.1 M Tris pH 8.0
Matthews coefficient: 2.11
Solvent content (%): 41.71
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: 2020-10-07
Crystal structure of human proheparanase, in complex with glucuronic acid configured aziridine probe JJB355 (PDB entry 5LA7)
Macromolecule: Heparanase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.1.166
Sequence length: 509 residues
Sequence: GQDVVDLDFFTQEPLHLVSPSFLSVTIDANLATDPRFLILLGSPKLRTLARGLSPAYLRFGGTKTDFLIFDPKKESTFEERSYWQSQVNQDICKYGSIPPDVEEKLRLEWPYQEQLLLREHYQKKFKNSTYSRSSVDVLYTFANCSGLDLIFGLNALLRTADLQWNSSNAQLLLDYCSSKGYNISWELGNEPNSFLKKADIFINGSQLGEDFIQLHKLLRKSTFKNAKLYGPDVGQPRRKTAKMLKSFLKAGGEVIDSVTWHHYYLNGRTATREDFLNPDVLDIFISSVQKVFQVVESTRPGKKVWLGETSSAYGGGAPLLSDTFAAGFMWLDKLGLSARMGIEVVMRQVFFGAGNYHLVDENFDPLPDYWLSLLFKKLVGTKVLMASVQGSKRRKLRVYLHCTNTDNPRYKEGDLTLYAINLHNVTKYLRLPYPFSNKQVDKYLLRPLGPHGLLSKSVQLNGLTLKMVDDQTLPPLMEKPLRPGSSLGLPAFSYSFFVIRNAKVAACI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.94
R work: 0.18205
R free: 0.22321
Average B factor: 46.254
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M Succinate pH 7.0
17% PEG3350
1:250 dilution seed stock

Seed crystals grown in 0.2 M Ammonium Nitrate, 20% PEG3350
Matthews coefficient: 2.27
Solvent content (%): 45.85
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: 2017-05-31
Crystal structure of HIS6-tagged Mdm2 with nutlin-3a (PDB entry 5Z02)
Macromolecule: E3 ubiquitin-protein ligase Mdm2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.27
Sequence length: 110 residues
Sequence: GSSHHHHHHSQDLENLYFQGSQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGDLFGVPSFSVKEHRKIYTMIYRNLVVVNQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.35
R work: 0.2258
R free: 0.2544
Average B factor: 24.094
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 0.2 Ammonium acetate, 20% ammonium sulfate
Matthews coefficient: 1.92
Solvent content (%): 36.02
Ligand: 4-({(4S,5R)-4,5-bis(4-chlorophenyl)-2-[4-methoxy-2-(propan-2-yloxy)phenyl]-4,5-dihydro-1H-imidazol-1-yl}carbonyl)piperazin-2-one (NUT)
Ligand formula: C30 H30 Cl2 N4 O4
Ligand molecular weight: 581.49
Ligand SMILES: CC(C)Oc1cc(ccc1C2=NC(C(N2C(=O)N3CCNC(=O)C3)c4ccc(cc4)Cl)c5ccc(cc5)Cl)OC
Ligand InChI: InChI=1S/C30H30Cl2N4O4/c1-18(2)40-25-16-23(39-3)12-13-24(25)29-34-27(19-4-8-21(31)9-5-19)28(20-6-10-22(32)11-7-20)36(29)30(38)35-15-14-33-26(37)17-35/h4-13,16,18,27-28H,14-15,17H2,1-3H3,(H,33,37)/t27-,28+/m0/s1
Release date: 2018-01-03
The Crystal structure of CK2a bound to P1-C4 (PDB entry 6Q38)
Macromolecule: Casein kinase II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 327 residues
Sequence: GPVPSRARVYTDVNTHRPSEYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.74
R work: 0.204
R free: 0.234
Average B factor: 56.92
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 298
Crystal growth procedure: 0.1 M HEPES 7.5 pH, 10 %w/v PEG 8K, 8 %v/v Ethelyene glycol
Matthews coefficient: 2.62
Solvent content (%): 53.04
Ligand: BENZOIC ACID (BEZ)
Ligand formula: C7 H6 O2
Ligand molecular weight: 122.121
Ligand SMILES: c1ccc(cc1)C(=O)O
Ligand InChI: InChI=1S/C7H6O2/c8-7(9)6-4-2-1-3-5-6/h1-5H,(H,8,9)
Release date: 2019-04-24
Structure of human DNA polymerase beta Host-Guest complex with the N7MG base paired with a dT (PDB entry 5DB7)
Macromolecule: DNA polymerase beta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 335 residues
Sequence: MSKRKAPQETLNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPSAARKFVDEGIKTLEDLRKNEDKLNHHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSESTKQPKLLHQVVEQLQKVHFITDTLSKGETKFMGVCQLPSKNDEKEYPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGEPLPVDSEKDIFDYIQWKYREPKDRSE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.209
R work: 0.2207
R free: 0.273
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 295
Crystal growth procedure: 14% to 23% PEG3400, and 350 mM sodium acetate in 50 mM imidazole (pH 7.5)
Matthews coefficient: 2.4
Solvent content (%): 48.67
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2015-11-11
Co-crystal structure of human PRMT9 in complex with MT556 inhibitor (PDB entry 7RBQ)
Macromolecule: Protein arginine N-methyltransferase 9
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.320
Sequence length: 719 residues
Sequence: AVKLNPDFSDAKENFYRVANWLVERWHFIMLNDTKRNTIYNAAIQKAVCLGSKSVLDIGAGTGILSMFAKKAGAHSVYACELSKTMYELACDVVAANKMEAGIKLLHTKSLDIEIPKHIPERVSLVVTETVDAGLFGEGIVESLIHAWEHLLLQPKTKGESANCEKYGKVIPASAVIFGMAVECAEIRRHHRVGIKDIAGIHLPTNVKFQSPAYSSVDTEETIEPYTTEKMSRVPGGYLALTECFEIMTVDFNNLQELKSLATKKPDKIGIPVIKEGILDAIMVWFVLQLDDEHSLSTSPSEETCWEQAVYPVQDLADYWIKPGDHVMMEVSCQDCYLRIQSISVLGLECEMDVAKSFTQNKDLLSLGNEAELCSALANLQTSKPDAVEQTCILESTEIALLNNIPYHEGFKMAMSKVLSSLTPEKLYQTMDTHCQNEMSSGTGQSNTVQNILEPFYVLDVSEGFSVLPVIAGTLGQVKPYSSVEKDQHRIALDLISEANHFPKETLEFWLRHVEDESAMLQRPKSDKLWSIIILDVIEPSGLIQQEIMEKAAISRCLLQSGGKIFPQYVLMFGLLVESQTLLEENAVQGTERTLGLNIAPFINQFQVPIRVFLDLSSLPCIPLSKPVELLRLDLMTPYLNTSNREVKVYVCKSGRLTAIPFWYHMYLDEEIRLDTSSEASHWKQAAVVLDNPIQVEMGEELVLSIQHHKSNVSITVKQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.2123
R free: 0.2706
Average B factor: 37.41
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 291
Crystal growth procedure: 25%(w/v)PEG3350, 0.1M Ammonium Sulphate, 0.1M Bis-Tris pH7.4
Matthews coefficient: 2.13
Solvent content (%): 42.23
Ligand: 7-[5-S-(4-{[(4-ethylpyridin-3-yl)methyl]amino}butyl)-5-thio-beta-D-ribofuranosyl]-7H-pyrrolo[2,3-d]pyrimidin-4-amine (44T)
Ligand formula: C23 H32 N6 O3 S
Ligand molecular weight: 472.604
Ligand SMILES: CCc1ccncc1CNCCCCSCC2C(C(C(O2)n3ccc4c3ncnc4N)O)O
Ligand InChI: InChI=1S/C23H32N6O3S/c1-2-15-5-8-26-12-16(15)11-25-7-3-4-10-33-13-18-19(30)20(31)23(32-18)29-9-6-17-21(24)27-14-28-22(17)29/h5-6,8-9,12,14,18-20,23,25,30-31H,2-4,7,10-11,13H2,1H3,(H2,24,27,28)/t18-,19-,20-,23-/m1/s1
Release date: 2021-08-11
Identification of an intermediate activation state of PAK5 reveals a novel mechanism of kinase inhibition. (PDB entry 8C12)
Macromolecule: Serine/threonine-protein kinase PAK 5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 295 residues
Sequence: MRVSHEQFRAALQLVVSPGDPREYLANFIKIGEGSTGIVCIATEKHTGKQVAVKKMDLRKQQRRELLFNEVVIMRDYHHDNVVDMYSSYLVGDELWVVMEFLEGGALTDIVTHTRMNEEQIATVCLSVLRALSYLHNQGVIHRDIKSDSILLTSDGRIKLSDFGFCAQVSKEVPKRKSLVGTPYWMAPEVISRLPYGTEVDIWSLGIMVIEMIDGEPPYFNEPPLQAMRRIRDSLPPRVKDLHKVSSVLRGFLDLMLVREPSQRATAQELLGHPFLKLAGPPSCIVPLMRQYRHH
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.549
R work: 0.1972
R free: 0.2341
Average B factor: 40.435
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 291
Crystal growth procedure: 0.12 M Alcohols (0.2 M 1,6-Hexanediol, 0.2 M 1-Butanol, 0.2 M 1,2_Propanediol, 0.2 M 2-Propanol, 0.2 M 1,4-Butanediol, 0.2 M 1,3-Propanediol), 0.1 M Buffer System 2 (1.0 M Sodium HEPES, MOPS) pH 7.5, 37.5% precipitant (M1K3350)
Matthews coefficient: 2.47
Solvent content (%): 50.11
Release date: 2023-10-25
HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with N-oxalylglycine (NOG) and a RaPID-derived silent allosteric cyclic peptide 3C (14-mer) (PDB entry 6YW4)
Macromolecule: Egl nine homolog 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11.29
Sequence length: 233 residues
Sequence: GSHMASPNGQTKPLPALKLALEYIVPAMNKHGICVVDDFLGKETGQQIGDEVRALHDTGKFTDGQLVSQKSDSSKDIRGDKITWIEGKEPGCETIGLLMSSMDDLIRHCNGKLGSYKINGRTKAMVACYPGNGTGYVRHVDNPNGDGRCVTCIYYLNKDWDAKVSGGILRIFPEGKAQFADIEPKFDRLLFFWSDRRNPHEVQPAYATRYAITVWYFDADERAAAKVKYLTGE
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.528
R work: 0.162
R free: 0.177
Average B factor: 34.4686
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: Sample: 1.0 mM cPHD2, 1.5 mM MnCl2, 2.0 mM compound, 1.0 mM 3C; Reservoir: 0.2 M lithium sulfate, 0.1 M Tris-HCl pH 8.5, 1.26 M ammonium sulfate; Sitting drop (300 nl), protein-to-well ratio, 1:1
Matthews coefficient: 2.56
Solvent content (%): 51.96
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: 2020-12-30
Cocrystal structure of the human acyl protein thioesterase 2 with an isoform-selective inhibitor, ML349 (PDB entry 5SYN)
Macromolecule: Acyl-protein thioesterase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.2
Sequence length: 231 residues
Sequence: MCGNTMSVPLLTDAATVSGAERETAAVIFLHGLGDTGHSWADALSTIRLPHVKYICPHAPRIPVTLNMKMVMPSWFDLMGLSPDAPEDEAGIKKAAENIKALIEHEMKNGIPANRIVLGGFSQGGALSLYTALTCPHPLAGIVALSCWLPLHRAFPQAANGSAKDLAILQCHGELDPMVPVRFGALTAEKLRSVVTPARVQFKTYPGVMHSSCPQEMAAVKEFLEKLLPPV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.64
R work: 0.22
R free: 0.25
Average B factor: 22.553
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 mM sodium citrate pH 5.5, 20-24% PEG 3350.
Matthews coefficient: 2.18
Solvent content (%): 43.56
Ligand: 2-[4-(4-methoxyphenyl)piperazine-1-carbonyl]-5lambda~6~-thieno[3,2-c][1]benzothiopyran-5,5(4H)-dione (71T)
Ligand formula: C23 H22 N2 O4 S2
Ligand molecular weight: 454.562
Ligand SMILES: COc1ccc(cc1)N2CCN(CC2)C(=O)c3cc4c(s3)-c5ccccc5S(=O)(=O)C4
Ligand InChI: InChI=1S/C23H22N2O4S2/c1-29-18-8-6-17(7-9-18)24-10-12-25(13-11-24)23(26)20-14-16-15-31(27,28)21-5-3-2-4-19(21)22(16)30-20/h2-9,14H,10-13,15H2,1H3
Release date: 2016-10-26
Crystal structure of human carbonic anhydrase II with 1-cyclopropyl-6-fluoro-4-oxo-7-(4-(4-sulfamoylbenzoyl)piperazin-1-yl)-1,4-dihydroquinoline-3-carboxylic acid (PDB entry 8OTP)
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): 1.4
R work: 0.1242
R free: 0.177
Average B factor: 16.103
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 296
Crystal growth procedure: 1.5 M sodium citrate, 0.1 M Tris pH 8.0
Matthews coefficient: 2.1
Solvent content (%): 41.49
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: 2024-05-01
Carbonic Anhydrase II in complex with Beta-Galactose-2C (PDB entry 7RRE)
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): 1.44
R work: 0.1467
R free: 0.1674
Average B factor: 16.3259
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 pH 7.8
Matthews coefficient: 2.09
Solvent content (%): 41.19
Ligand: 2-[1-(1,1,3-trioxo-2,3-dihydro-1H-1lambda~6~,2-benzothiazol-6-yl)-1H-1,2,3-triazol-4-yl]ethyl beta-L-gulopyranoside (6IV)
Ligand formula: C17 H20 N4 O9 S
Ligand molecular weight: 456.427
Ligand SMILES: c1cc2c(cc1n3cc(nn3)CCOC4C(C(C(C(O4)CO)O)O)O)S(=O)(=O)NC2=O
Ligand InChI: InChI=1S/C17H20N4O9S/c22-7-11-13(23)14(24)15(25)17(30-11)29-4-3-8-6-21(20-18-8)9-1-2-10-12(5-9)31(27,28)19-16(10)26/h1-2,5-6,11,13-15,17,22-25H,3-4,7H2,(H,19,26)/t11-,13+,14-,15-,17-/m0/s1
Release date: 2022-08-24
Crystal structure of human FSP1 (PDB entry 8WIK)
Macromolecule: Ferroptosis suppressor protein 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.6.5
Sequence length: 373 residues
Sequence: MGSQVSVESGALHVVIVGGGFGGIAAASQLQALNVPFMLVDMKDSFHHNVAALRASVETGFAKKTFISYSVTFKDNFRQGLVVGIDLKNQMVLLQGGEALPFSHLILATGSTGPFPGKFNEVSSQQAAIQAYEDMVRQVQRSRFIVVVGGGSAGVEMAAEIKTEYPEKEVTLIHSQVALADKELLPSVRQEVKEILLRKGVQLLLSERVSNLEELPLNEYREYIKVQTDKGTEVATNLVILCTGIKINSSAYRKAFESRLASSGALRVNEHLQVEGHSNVYAIGDCADVRTPKMAYLAGLHANIAVANIVNSVKQRPLQAYKPGALTFLLSMGRNDGVGQISGFYVGRLMVRLTKSRDLFVSTSWKTMRQSPP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.2245
R free: 0.2627
Average B factor: 35.59
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291
Crystal growth procedure: HEPES , MgCl2, PEG3350
Matthews coefficient: 2.93
Solvent content (%): 58.05
Ligand: 6-HYDROXY-FLAVIN-ADENINE DINUCLEOTIDE (6FA)
Ligand formula: C27 H33 N9 O16 P2
Ligand molecular weight: 801.549
Ligand SMILES: Cc1cc2c(c(c1C)O)N=C3C(=O)NC(=O)N=C3N2CC(C(C(COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)O
Ligand InChI: InChI=1S/C27H33N9O16P2/c1-9-3-11-15(18(39)10(9)2)32-17-24(33-27(44)34-25(17)43)35(11)4-12(37)19(40)13(38)5-49-53(45,46)52-54(47,48)50-6-14-20(41)21(42)26(51-14)36-8-31-16-22(28)29-7-30-23(16)36/h3,7-8,12-14,19-21,26,37-42H,4-6H2,1-2H3,(H,45,46)(H,47,48)(H2,28,29,30)(H,34,43,44)/t12-,13+,14+,19-,20+,21+,26+/m0/s1
Release date: 2024-05-08
Crystal structure of the TgGalNAc-T3 in complex with UDP, manganese and the peptide 3 (PDB entry 6S24)
Macromolecule: Polypeptide N-acetylgalactosaminyltransferase
Type: Protein, polypeptide(L)
Source organism: Taeniopygia guttata
EC number: 2.4.1
Sequence length: 631 residues
Sequence: MALKKAPKLFKTFFHWKLWKFSIIVFVFLVFLFLLQREVGVQDFKDEAGIEPVVGKKSHVLGLVLNAMNNIKGAKPKMQIKAPIRQTKVPGERHCLPGHYTPVELKPFLDRPLQDPNAPGASGKAFKTINLNSEEQKEKQAGEEKHCFNAFASDRISLHRDLGPDTRPPECIEQKFKRCPPLPTTSIIIVFHNEAWSTLLRTVHSVMYTSPAILLKEIILVDDASVDEYLHDKLDEYVKQFQIVKVVRQKERKGLITARLLGASVATGETLTFLDAHCECFYGWLEPLLARIAENPVAVVSPDIASIDLNTFEFSKPSPYGHSHNRGNFDWSLSFGWESLPKHENKRRKDETYPIRTPTFAGGLFSISKDYFEYIGSYDEEMEIWGGENIEMSFRVWQCGGQLEIMPCSVVGHVFRSKSPHTFPKGTQVITRNQVRLAEVWMDEYKEIFYRRNTEAAKIVKQKTFGDISKRIDLRQRLQCKNFTWYLSNVYPEAYVPDLNPLFSGYLKNIGNRMCLDVGENNHGGKPLIMYSCHGLGGNQYFEYSAHHEIRHNIQKELCLHASKGPVQLRECTYKGQKTFAVGEEQWLHQKDQTLYNEALHMCLTGNGEHPSLASCNPSDPFQKWIFGQND
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.12
R work: 0.19119
R free: 0.23738
Average B factor: 41.609
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: Morpheus precipitant mix 4, nitrate phosphate buffer and Morpheus buffer System 1
Matthews coefficient: 2.56
Solvent content (%): 52.02
Ligand: TRIS(HYDROXYETHYL)AMINOMETHANE (TAM)
Ligand formula: C7 H17 N O3
Ligand molecular weight: 163.215
Ligand SMILES: C(CO)C(CCO)(CCO)N
Ligand InChI: InChI=1S/C7H17NO3/c8-7(1-4-9,2-5-10)3-6-11/h9-11H,1-6,8H2
Release date: 2019-12-25
Structure of M1-StaR-T4L in complex with HTL0009936 at 2.35A (PDB entry 6ZG4)
Macromolecule: Muscarinic acetylcholine receptor M1,Endolysin,Muscarinic acetylcholine receptor M1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.1.17
Sequence length: 455 residues
Sequence: METVEMVAIATVAGLLSLATVTGNILLMLSIKVNRQLQTVNNYFAFSLACADLIIGAFSMNLYTVYIIMGHWALGALACDLALALDYVASNAAVMNLLLISFDRYFSVTRPLSYRAKRTPRRALLMIGLAWLVSFVLWAPAILFWQYLVGERTVLAGQCYIQFLSQPIITFGTAMATFYLPVTVMCTLYWRIYRETENRANIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYTFSLVKEKAALRTLSAILLAFILTWTPYNIMVLVSTFCKDCVPETLWELGYWLCYVNATINPMCYALCNKAFRDTFRLLLLARWDHHHHHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.33
R work: 0.204
R free: 0.234
Average B factor: 35.72
Crystallization method: LIPIDIC CUBIC PHASE
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M NaHEPES pH 7.4-7.8, 0.1M di-Ammonium hydrogenphosphate, 30-38% PEG300
Matthews coefficient: 3.05
Solvent content (%): 59.72
Ligand: ethyl (4~{S})-4-[4-[(1-methylcyclobutyl)carbamoyl]piperidin-1-yl]azepane-1-carboxylate (QK8)
Ligand formula: C20 H35 N3 O3
Ligand molecular weight: 365.51
Ligand SMILES: CCOC(=O)N1CCCC(CC1)N2CCC(CC2)C(=O)NC3(CCC3)C
Ligand InChI: InChI=1S/C20H35N3O3/c1-3-26-19(25)23-12-4-6-17(9-15-23)22-13-7-16(8-14-22)18(24)21-20(2)10-5-11-20/h16-17H,3-15H2,1-2H3,(H,21,24)/t17-/m0/s1
Release date: 2021-10-06
Crystal structure of human polymerase eta inserting dAMPnPP opposite DNA template containing an abasic site (PDB entry 4RNM)
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): 2.144
R work: 0.167
R free: 0.219
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, 25% PEG 2000 MME 
, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K
Matthews coefficient: 2.1
Solvent content (%): 41.38
Ligand: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine (DZ4)
Ligand formula: C10 H17 N6 O11 P3
Ligand molecular weight: 490.197
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3CC(C(O3)COP(=O)(NP(=O)(O)OP(=O)(O)O)O)O)N
Ligand InChI: InChI=1S/C10H17N6O11P3/c11-9-8-10(13-3-12-9)16(4-14-8)7-1-5(17)6(26-7)2-25-28(18,19)15-29(20,21)27-30(22,23)24/h3-7,17H,1-2H2,(H2,11,12,13)(H2,22,23,24)(H3,15,18,19,20,21)/t5-,6+,7+/m0/s1
Release date: 2015-02-18
Crystal structure of OspC3-calmodulin-caspase-4 complex (PDB entry 7WR4)
Macromolecule: Calmodulin-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 149 residues
Sequence: MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.75
R work: 0.2321
R free: 0.2698
Average B factor: 93.86
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 25% PEG3350, 0.1 M HEPES pH 7.4, 0.2 M Ammonium sulfate, 0.3 M NDSB-195
Matthews coefficient: 2.66
Solvent content (%): 53.72
Release date: 2023-01-25
Predicting the Conformational Variability of Abl Tyrosine Kinase Using Molecular Dynamics Simulations and Markov State Models (PDB entry 6BL8)
Macromolecule: Tyrosine-protein kinase ABL1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 272 residues
Sequence: DKWEMERTDITMKHKLGGGQYGEVYEGVWKKYSLTVAVKTLKEDTMEVEEFLKEAAVMKEIKHPNLVQLLGVCTREPPFYIITEFMTYGNLLDYLRECNRQEVSAVVLLYMATQISSAMEYLEKKNFIHRDLAARNCLVGENHLVKVADFGLSRLMTGDTFTAHAGAKFPIKWTAPESLAYNKFSIKSDVWAFGVLLWEIATYGMSPYPGIDPSQVYELLEKDYRMERPEGCPEKVYELMRACWQWNPSDRPSFAEIHQAFETMFQESSISD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.175
R free: 0.204
Average B factor: 43.44
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 295
Crystal growth procedure: 100 mM sodium citrate, pH 5.6, 1850 mM ammonium sulfate, 140 mM potassium sodium tartrate
Matthews coefficient: 3.16
Solvent content (%): 61.13
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: 2018-03-07
DHODH IN COMPLEX WITH LIGAND 29 (PDB entry 8DHH)
Macromolecule: Dihydroorotate dehydrogenase (quinone), mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.3.5.2
Sequence length: 369 residues
Sequence: GAMATGDERFYAEHLMPTLQGLLDPESAHRLAVRFTSLGLLPRARFQDSDMLEVRVLGHKFRNPVGIAAGFDKHGEAVDGLYKMGFGFVEIGSVTPKPQEGNPRPRVFRLPEDQAVINRYGFNSHGLSVVEHRLRARQQKQAKLTEDGLPLGVNLGKNKTSVDAAEDYAEGVRVLGPLADYLVVNVSSPNTAGLRSLQGKAELRRLLTKVLQERDGLRRVHRPAVLVKIAPDLTSQDKEDIASVVKELGIDGLIVTNTTVSRPAGLQGALRSETGGLSGKPLRDLSTQTIREMYALTQGRVPIIGVGGVSSGQDALEKIRAGASLVQLYTALTFWGPPVVGKVKRELEALLKEQGFGGVTDAIGADHRR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.02
R work: 0.1856
R free: 0.2156
Average B factor: 39.505
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 4.8
Crystallization temperature (K): 293
Crystal growth procedure: 0.10 M Sodium Acetate pH4.8, 2.30 M (NH4)2SO4, 30% Glycerol
Matthews coefficient: 3.61
Solvent content (%): 65.92
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: 2022-08-17