satarupa22/MacromolecularLigandDB huggingface dataset:
PanDDA analysis group deposition of ground-state model of PTP1B, using pre-clustering, cluster7 (PDB entry 7GU1)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 321 residues
Sequence: MEMEKEFEQIDKSGSWAAIYQDIRHEASDFPSRVAKLPKNKNRNRYRDVSPFDHSRIKLHQEDNDYINASLIKMEEAQRSYILTQGPLPNTVGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQKEEKEMIFEDTNLKLTLISEDIKSYYTVRQLELENLTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRESGSLSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKDPSSVDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFIMGDSSVQDQWKELSHEDLEPPPEHIPPPPRPPKRILEPHN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.59
R work: 0.1987
R free: 0.2174
Average B factor: 39.0015
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.3 M magnesium acetate, 0.1 M HEPES pH 7.5, 0.1% beta-mercaptoethanol, 13-14% PEG 8000, 2% ethanol
Matthews coefficient: 3.35
Solvent content (%): 63.28
Ligand: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL (TRS)
Ligand formula: C4 H12 N O3
Ligand molecular weight: 122.143
Ligand SMILES: C(C(CO)(CO)[NH3+])O
Ligand InChI: InChI=1S/C4H11NO3/c5-4(1-6,2-7)3-8/h6-8H,1-3,5H2/p+1
Release date: 2024-01-31
HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with 2OG and RaPID-derived silent allosteric cyclic peptide 3C (14-mer) (PDB entry 6YW1)
Macromolecule: Egl nine homolog 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11.29
Sequence length: 233 residues
Sequence: GSHMASPNGQTKPLPALKLALEYIVPCMNKHGICVVDDFLGKETGQQIGDEVRALHDTGKFTDGQLVSQKSDSSKDIRGDKITWIEGKEPGCETIGLLMSSMDDLIRHCNGKLGSYKINGRTKAMVACYPGNGTGYVRHVDNPNGDGRCVTCIYYLNKDWDAKVSGGILRIFPEGKAQFADIEPKFDRLLFFWSDRRNPHEVQPAYATRYAITVWYFDADERARAKVKYLTGE
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.46
R work: 0.1642
R free: 0.1746
Average B factor: 34.1839
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: Sample: 1.0 mM PHD2, 1.5 mM MnCl2, 2.0 mM compound, 1.0 mM 3C; Reservoir: 0.1 M Bis-Tris pH 6.5, 15.0 % PEG 3350, 0.002 M MnCl2; Sitting drop (300 nl), protein-to-well ratio, 1:2
Matthews coefficient: 2.53
Solvent content (%): 51.41
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
Carbonic Anhydrase II in complex with the alkyl urea 3h (PDB entry 8FQY)
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): 1.466
R work: 0.1686
R free: 0.1854
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 base
Matthews coefficient: 2.03
Solvent content (%): 39.54
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: 2023-02-01
Structure of SARS-CoV-2 Gamma variant receptor-binding domain complexed with high affinity human ACE2 mutant (T27F,R273Q) (PDB entry 7WNM)
Macromolecule: Angiotensin-converting enzyme 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.17.23
Sequence length: 740 residues
Sequence: MSSSSWLLLSLVAVTAAQSTIEEQAKFFLDKFNHEAEDLFYQSSLASWNYNTNITEENVQNMNNAGDKWSAFLKEQSTLAQMYPLQEIQNLTVKLQLQALQQNGSSVLSEDKSKRLNTILNTMSTIYSTGKVCNPDNPQECLLLEPGLNEIMANSLDYNERLWAWESWRSEVGKQLRPLYEEYVVLKNEMARANHYEDYGDYWRGDYEVNGVDGYDYSRGQLIEDVEHTFEEIKPLYEHLHAYVRAKLMNAYPSYISPIGCLPAHLLGDMWGQFWTNLYSLTVPFGQKPNIDVTDAMVDQAWDAQRIFKEAEKFFVSVGLPNMTQGFWENSMLTDPGNVQKAVCHPTAWDLGKGDFRILMCTKVTMDDFLTAHHEMGHIQYDMAYAAQPFLLRNGANEGFHEAVGEIMSLSAATPKHLKSIGLLSPDFQEDNETEINFLLKQALTIVGTLPFTYMLEKWRWMVFKGEIPKDQWMKKWWEMKREIVGVVEPVPHDETYCDPASLFHVSNDYSFIRYYTRTLYQFQFQEALCQAAKHEGPLHKCDISNSTEAGQKLFNMLRLGKSEPWTLALENVVGAKNMNVRPLLNYFEPLFTWLKDQNKNSFVGWSTDWSPYADQSIKVRISLKSALGDKAYEWNDNEMYLFRSSVAYAMRQYFLKVKNQMILFGEEDVRVANLKPRISFNFFVTAPKNVSDIIPRTEVEKAIRMSRSRINDAFRLNDNSLEFLGIQPTLGPPNQPPVS
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.7
R work: 0.1938
R free: 0.2225
Average B factor: 43.88
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6
Crystallization temperature (K): 291
Crystal growth procedure: 0.1 M magnesium chloride, 0.1 M MES (pH 6.0) and 8% w/v polyethylene glycol 6000
Matthews coefficient: 2.81
Solvent content (%): 56
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: 2022-12-21
Structure of human DNA polymerase beta complexed with 8-ClG in the template base paired with incoming non-hydrolyzable ATP and MANGANESE (PDB entry 6CUB)
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): 2.05
R work: 0.1966
R free: 0.2541
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 14% to 23% PEG3400, and 350 mM sodium acetate in 50 mM imidazole (pH 7.5)
Matthews coefficient: 2.38
Solvent content (%): 48.26
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: 2019-03-27
Crystal structure of MYST acetyltransferase domain in complex with inhibitor 40 (PDB entry 6PDE)
Macromolecule: Histone acetyltransferase KAT8
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 272 residues
Sequence: KYVDKIHIGNYEIDAWYFSPFPEDYGKQPKLWLCEYCLKYMKYEKSYRFHLGQCQWRQPPGKEIYRKSNISVHEVDGKDHKIYCQNLCLLAKLFLDHKTLYFDVEPFVFYILTEVDRQGAHIVGYFSKEKESPDGNNVSCIMILPPYQRRGYGRFLIAFSYELSKLESTVGSPEKPLSDLGKLSYRSYWSSVLLENLRDFRGTLSIKDLSQMTSITQNDIISTLQSLNMVKYWKGQHVICVTPKLVEEHLKSAQYKKPPITVDSVCLKWAPP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.22
R work: 0.1823
R free: 0.2093
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 292
Crystal growth procedure: 27% PEG 3350, 0.2 M ammonium sulfate, 0.1 M bis-tris pH 6.5
Matthews coefficient: 2.49
Solvent content (%): 50.7
Ligand: 2-fluoro-3-methyl-N'-(phenylsulfonyl)-5-propoxybenzohydrazide (O9V)
Ligand formula: C17 H19 F N2 O4 S
Ligand molecular weight: 366.407
Ligand SMILES: CCCOc1cc(c(c(c1)C(=O)NNS(=O)(=O)c2ccccc2)F)C
Ligand InChI: InChI=1S/C17H19FN2O4S/c1-3-9-24-13-10-12(2)16(18)15(11-13)17(21)19-20-25(22,23)14-7-5-4-6-8-14/h4-8,10-11,20H,3,9H2,1-2H3,(H,19,21)
Release date: 2020-04-01
CLK1 bound with beta-carboline KH-CARB13 (Cpd 3) (PDB entry 6YTG)
Macromolecule: Dual specificity protein kinase CLK1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 339 residues
Sequence: SMHLICQSGDVLSARYEIVDTLGEGAFGKVVECIDHKAGGRHVAVKIVKNVDRYCEAARSEIQVLEHLNTTDPNSTFRCVQMLEWFEHHGHICIVFELLGLSTYDFIKENGFLPFRLDHIRKMAYQICKSVNFLHSNKLTHTDLKPENILFVQSDYTEAYNPKIKRDERTLINPDIKVVDFGSATYDDEHHSTLVSTRHYRAPEVILALGWSQPCDVWSIGCILIEYYLGFTVFPTHDSKEHLAMMERILGPLPKHMIQKTRKRKYFHHDRLDWDEHSSAGRYVSRACKPLKEFMLSQDVEHERLFDLIQKMLEYDPAKRITLREALKHPFFDLLKKSI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.95
R work: 0.2037
R free: 0.2609
Average B factor: 27.064
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8
Crystallization temperature (K): 277
Crystal growth procedure: 17% PEG 6k, 0.1M bicine
Matthews coefficient: 2.54
Solvent content (%): 51.59
Ligand: (4~{S})-7,8-bis(chloranyl)-9-methyl-1-oxidanylidene-spiro[2,4-dihydropyrido[3,4-b]indole-3,4'-piperidine]-4-carbonitrile (KHC)
Ligand formula: C17 H16 Cl2 N4 O
Ligand molecular weight: 363.241
Ligand SMILES: Cn1c2c(ccc(c2Cl)Cl)c3c1C(=O)NC4(C3C#N)CCNCC4
Ligand InChI: InChI=1S/C17H16Cl2N4O/c1-23-14-9(2-3-11(18)13(14)19)12-10(8-20)17(4-6-21-7-5-17)22-16(24)15(12)23/h2-3,10,21H,4-7H2,1H3,(H,22,24)/t10-/m0/s1
Release date: 2020-07-15
Crystal structure of human AKR1B10 complexed with NADP+ and the inhibitor MK184 (PDB entry 5LIX)
Macromolecule: Aldo-keto reductase family 1 member B10
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.1.1
Sequence length: 316 residues
Sequence: MATFVELSTKAKMPIVGLGTWKSPLGKVKEAVKVAIDAGYRHIDCAYVYQNEHEVGEAIQEKIQEKAVKREDLFIVSKLWPTFFERPLVRKAFEKTLKDLKLSYLDVYLIHWPQGFKSGDDLFPRDDKGNAIGGKATFLDAWEAMEELVDEGLVKALGVSNFSHFQIEKLLNKPGLKYKPVTNQVECHPYLTQEKLIQYCHSKGITVTAYSPLGSPDRPWAKPEDPSLLEDPKIKEIAAKHKKTAAQVLIRFHIQRNVIVIPKSVTPARIVENIQVFDFKLSDEEMATILSFNRNWRACNLLQSSHLEDYPFNAEY
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.95
R work: 0.1948
R free: 0.2433
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 9
Crystallization temperature (K): 293
Crystal growth procedure: 30% PEG 6000, 100 mM sodium cacodylate
Matthews coefficient: 2.51
Solvent content (%): 51.05
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: 2016-07-27
Crystal structure of COQ8A-CA157 inhibitor complex in space group P1 (PDB entry 7UDQ)
Macromolecule: Atypical kinase COQ8A, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7
Sequence length: 393 residues
Sequence: SSEANAERIVRTLCKVRGAALKLGQMLSIQDDAFINPHLAKIFERVRQSADFMPLKQMMKTLNNDLGPNWRDKLEYFEERPFAAASIGQVHLARMKGGREVAMKIQYPGVAQSINSDVNNLMAVLNMSNMLPEGLFPEHLIDVLRRELALECDYQREAACARKFRDLLKGHPFFYVPEIVDELCSPHVLTTELVSGFPLDQAEGLSQEIRNEICYNILVLCLRELFEFHFMQTDPNWSNFFYDPQQHKVALLDFGATREYDRSFTDLYIQIIRAAADRDRETVRAKSIEMKFLTGYEVKVMEDAHLDAILILGEAFASDEPFDFGTQSTTEKIHNLIPVMLRHRLVPPPEETYSLHRKMGGSFLICSKLKARFPCKAMFEEAYSNYCKRQAQQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.1916
R free: 0.2387
Average B factor: 61.8219
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: Crystals were grown in a MRC SD2 plate set by a STP Labtech Mosquito. Protein at 17.89 mg/ml (390 uM) was incubated with 500 uM CA157 for 30 min at ambient temperature prior to setup. The drop producing this data set was 200 nL protein-CA157 solution was mixed with 300 nL of 0.6 M sodium succinate, pH 7
Matthews coefficient: 2.19
Solvent content (%): 43.86
Ligand: 4-[(3,4,5-trimethoxyphenyl)amino]quinoline-7-carbonitrile (MVS)
Ligand formula: C19 H17 N3 O3
Ligand molecular weight: 335.357
Ligand SMILES: COc1cc(cc(c1OC)OC)Nc2ccnc3c2ccc(c3)C#N
Ligand InChI: InChI=1S/C19H17N3O3/c1-23-17-9-13(10-18(24-2)19(17)25-3)22-15-6-7-21-16-8-12(11-20)4-5-14(15)16/h4-10H,1-3H3,(H,21,22)
Release date: 2023-01-18
Crystal structure of monoubiquitinated TRIM21 RING (Ub-RING) In complex with ubiquitin charged Ube2N (Ube2N~Ub) and Ube2V2 (PDB entry 7BBD)
Macromolecule: Polyubiquitin-B,E3 ubiquitin-protein ligase TRIM21
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.27
Sequence length: 164 residues
Sequence: GSHMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRAAMASAARLTMMWEEVTCPICLDPFVEPVSIECGHSFCQECISQVGKGGGSVCPVCRQRFLLKNLRPNRQLANMVNNLKEISQEARE
Oligomeric state: Hetero 4-mer
Stoichiometry: A1, B1, C1, D1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.222
R free: 0.2524
Average B factor: 52.09
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 290.15
Crystal growth procedure: MOPSO, Bis-Tris, PEG 4K, 1,2,6-hexanetriol, Li, Na, K
Matthews coefficient: 3.22
Solvent content (%): 61.75
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: 2021-01-27
PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of HAO1 in complex with Z2697514548 (PDB entry 5QIH)
Macromolecule: Hydroxyacid oxidase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.1.3.15
Sequence length: 369 residues
Sequence: SMLPRLICINDYEQHAKSVLPKSIYDYYRSGANDEETLADNIAAFSRWKLYPRMLRNVAETDLSTSVLGQRVSMPICVGATAMQRMAHVDGELATVRACQSLGTGMMLSSWATSSIEEVAEAGPEALRWLQLYIYKDREVTKKLVRQAEKMGYKAIFVTVDTPYLGNRLDDVRNRFKLPPQLRMKNFETSTLSFSPEENFGDDSGLAAYVAKAIDPSISWEDIKWLRRLTSLPIVAKGILRGDDAREAVKHGLNGILVSNHGARQLDGVPATIDVLPEIVEAVEGKVEVFLDGGVRKGTDVLKALALGAKAVFVGRPIVWGLAFQGEKGVQDVLEILKEEFRLAMALSGCQNVKVIDKTLVRKNPLAVS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.33
R work: 0.179
R free: 0.1981
Average B factor: 18.571
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.75
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M MIB pH 5.75 - 7.0, 27.5-35% PEG1000
Matthews coefficient: 2.34
Solvent content (%): 47.48
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: 2018-07-18
Crystal structure of MOZ double PHD finger in complex with histone H3 butyrylation at K14 (PDB entry 5B75)
Macromolecule: Histone acetyltransferase KAT6A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 131 residues
Sequence: SLPHEKDKPVAEPIPICSFCLGTKEQNREKKPEELISCADCGNSGHPSCLKFSPELTVRVKALRWQCIECKTCSSCRDQGKNADNMLFCDSCDRGFHMECCDPPLTRMPKGMWICQICRPRKKGRKLLQKK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.704
R work: 0.1696
R free: 0.195
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 290
Crystal growth procedure: polyethylene glycol 4000, lithium sulfate, Tris
Matthews coefficient: 2.48
Solvent content (%): 50.37
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: 2016-10-26
The Crystal Structure of SHP1 from Biortus. (PDB entry 8YHI)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 6
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 288 residues
Sequence: GSGFWEEFESLQKQEVKNLHQRLEGQRPENKGKNRYKNILPFDHSRVILQGRDSNIPGSDYINANYIKNQLLGPDENAKTYIASQGCLEATVNDFWQMAWQENSRVIVMTTREVEKGRNKCVPYWPEVGMQRAYGPYSVTNCGEHDTTEYKLRTLQVSPLDNGDLIREIWHYQYLSWPDHGVPSEPGGVLSFLDQINQRQESLPHAGPIIVHSSAGIGRTGTIIVIDMLMENISTKGLDCDIDIQKTIQMVRAQRSGMVQTEAQYKFIYVAIAQFIETTKKKLEVLQS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.75
R work: 0.1925
R free: 0.2266
Average B factor: 30.129
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M Hepes  pH7.5, 2% PEG 400, 2.0M (NH4)2SO4
Matthews coefficient: 2.14
Solvent content (%): 42.61
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: 2024-03-13
Structure of the mitogen activated kinase kinase 7 in complex with pyrazolopyrimidine inhibitor 1h (PDB entry 6QG4)
Macromolecule: Dual specificity mitogen-activated protein kinase kinase 7
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.2
Sequence length: 318 residues
Sequence: MGHHHHHHSAKQTGYLTIGGQRYQAEINDLENLGEMGSGTCGQVWKMRFRKTGHVIAVKQMRRSGNKEENKRILMDLDVVLKSHDCPYIVQCFGTFITNTDVFIAMELMGTCAEKLKKRMQGPIPERILGKMTVAIVKALYYLKEKHGVIHRDVKPSNILLDERGQIKLCDFGISGRLVDSKAKTRSAGCAAYMAPERIDPPDPTKPDYDIRADVWSLGISLVELATGQFPYKNCKTDFEVLTKVLQEEPPLLPGHMGFSGDFQSFVKDCLTKDHRKRPKYNKLLEHSFIKRYETLEVDVASWFKDVMAKTESPRTSG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.2339
R free: 0.2691
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.2 M Sodiumcitrate
0.2% PEG3350
Matthews coefficient: 2.4
Solvent content (%): 48.79
Ligand: 1-[(3~{R})-3-[4-azanyl-3-(4-hydroxyphenyl)pyrazolo[3,4-d]pyrimidin-1-yl]piperidin-1-yl]propan-1-one (J0E)
Ligand formula: C19 H22 N6 O2
Ligand molecular weight: 366.417
Ligand SMILES: CCC(=O)N1CCCC(C1)n2c3c(c(n2)c4ccc(cc4)O)c(ncn3)N
Ligand InChI: InChI=1S/C19H22N6O2/c1-2-15(27)24-9-3-4-13(10-24)25-19-16(18(20)21-11-22-19)17(23-25)12-5-7-14(26)8-6-12/h5-8,11,13,26H,2-4,9-10H2,1H3,(H2,20,21,22)/t13-/m1/s1
Release date: 2019-05-22
Human DNA Polymerase Beta With Gapped DNA Containing an 8-oxo-7,8-dihydro-Guanine (8-oxoG)and dCTP soaked with MnCl2 for 35 s (PDB entry 4RQ2)
Macromolecule: DNA polymerase beta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 343 residues
Sequence: MGMSKRKAPQETLNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPSAARKFVDEGIKTLEDLRKNEDKLNHHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSESTKQPKLLHQVVEQLQKVHFITDTLSKGETKFMGVCQLPSKNDEKEYPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGEPLPVDSEKDIFDYIQWKYREPKDRSEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.19404
R free: 0.26868
Average B factor: 35.986
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 295
Crystal growth procedure: 50 MM IMIDAZOLE, 350 MM SODIUM Acetate, 17% PEG3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Matthews coefficient: 2.14
Solvent content (%): 42.52
Ligand: PYROPHOSPHATE (PPV)
Ligand formula: H4 O7 P2
Ligand molecular weight: 177.975
Ligand SMILES: OP(=O)(O)OP(=O)(O)O
Ligand InChI: InChI=1S/H4O7P2/c1-8(2,3)7-9(4,5)6/h(H2,1,2,3)(H2,4,5,6)
Release date: 2015-04-15
Crystal structure of the kinase domain of human c-KIT in complex with a type-II inhibitor bearing an acrylamide (PDB entry 6XVA)
Macromolecule: Mast/stem cell growth factor receptor Kit,Mast/stem cell growth factor receptor Kit
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 328 residues
Sequence: GSHMPMYEVQWKVVEESNGNNYSYIDPTQLPYDHKWEFPRNRLSFGKTLGAGAFGKVVEATAQGLIKSDAAMTVAVKMLKPSAHSTEREALMSELKVLSYLGNHENIVNLLGACTHGGPTLVITEYCCYGDLLNFLRRKRDEFVPYKVAPEDLYKDFLTLEHLLSFSYQVAKGMAFLASKNCIHRDLAARNILLTHGNITKICDFGLARDIKNDSNYVDKGNARLPVKWMAPESIFNSVYTFESDVWSYGIFLWELFSLGSSPYPGMPVDSKFYKMIKEGFRMSSPEYAPAEMYDIMKTCWDADPDKRPTFKQIVQDIEKQISESTNH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.196
R free: 0.245
Average B factor: 51.86
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 10 % PEG4000, 20 % glycerol, 10 % MORPHEUS carboxylic acids, 0.1 M HEPES-MOPS buffer pH 7.5
Matthews coefficient: 2.41
Solvent content (%): 48.99
Ligand: ~{N}-[[3-[2-[3-methoxy-5-(7-methoxyquinolin-4-yl)oxy-pyridin-2-yl]ethanoylamino]-5-methyl-phenyl]methyl]propanamide (O2K)
Ligand formula: C29 H30 N4 O5
Ligand molecular weight: 514.572
Ligand SMILES: CCC(=O)NCc1cc(cc(c1)NC(=O)Cc2c(cc(cn2)Oc3ccnc4c3ccc(c4)OC)OC)C
Ligand InChI: InChI=1S/C29H30N4O5/c1-5-28(34)32-16-19-10-18(2)11-20(12-19)33-29(35)15-25-27(37-4)14-22(17-31-25)38-26-8-9-30-24-13-21(36-3)6-7-23(24)26/h6-14,17H,5,15-16H2,1-4H3,(H,32,34)(H,33,35)
Release date: 2020-05-27
Protein Kinase A in complex with an Inhibitor (PDB entry 4UJ1)
Macromolecule: CAMP-DEPENDENT PROTEIN KINASE CATALYTIC SUBUNIT ALPHA
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.11
Sequence length: 351 residues
Sequence: MGNAAAAKKGSEQESVKEFLAKAKEDFLKKWESPAQNTAHLDQFERIKTLGTGSFGRVMLVKHKETGNHYAMKILDKQKVVKLKQIEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLYMVMEYVPGGEMFSHLRRIGRFSEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLLIDQQGYIQVTDFGFAKRVKGRTWTLCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKVRFPSHFSSDLKDLLRNLLQVDLTKRFGNLKNGVNDIKNHKWFATTDWIAIYQRKVEAPFIPKFKGPGDTSNFDDYEEEEIRVSINEKCGKEFSEF
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.768
R work: 0.1665
R free: 0.2014
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 10MG/ML PROTEIN, 25MM BISTRIS/MES PH6.9, 50MM KCL, 1.5MM OCTANOYL-N-METHYLGLUCAMIDE, 1MM PROTEIN KINASE INHIBITOR PEPTIDE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K
Matthews coefficient: 2.55
Solvent content (%): 51.81
Ligand: 7-[(3S,4R)-4-(3-chlorophenyl)carbonylpyrrolidin-3-yl]-3H-quinazolin-4-one (NVX)
Ligand formula: C19 H16 Cl N3 O2
Ligand molecular weight: 353.802
Ligand SMILES: c1cc(cc(c1)Cl)C(=O)C2CNCC2c3ccc4c(c3)N=CNC4=O
Ligand InChI: InChI=1S/C19H16ClN3O2/c20-13-3-1-2-12(6-13)18(24)16-9-21-8-15(16)11-4-5-14-17(7-11)22-10-23-19(14)25/h1-7,10,15-16,21H,8-9H2,(H,22,23,25)/t15-,16+/m1/s1
Release date: 2016-04-13
Coagulation Factor XII protease domain crystal structure (PDB entry 4XDE)
Macromolecule: Coagulation factor XII
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.38
Sequence length: 257 residues
Sequence: RSVVGGLVALRGAHPYIAALYWGHSFCAGSLIAPCWVLTAAHCLQDRPAPEDLTVVLGQERRNHSCEPCQTLAVRSYRLHEAFSPVSYQHDLALLRLQEDADGSCALLSPYVQPVSLPSGAARPSETTLCQVAGWGHQFEGAEEYASFLQEAQVPFLSLERCSAPDVHGSSILPGMLCAGFLEGGTDACQGDSGGPLVCEDQAAERRLTLQGIISWGSGCGDRNKPGVYTDVAYYLAWIREHTVSHHTGTRHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.14
R work: 0.22223
R free: 0.26235
Average B factor: 29.211
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 1.2 M Ammonium sulphate, 0.05 M tri-sodium citrate, 3%(w/v) isopropanol.
Matthews coefficient: 2.64
Solvent content (%): 53.33
Ligand: CITRATE ANION (FLC)
Ligand formula: C6 H5 O7
Ligand molecular weight: 189.1
Ligand SMILES: C(C(=O)[O-])C(CC(=O)[O-])(C(=O)[O-])O
Ligand InChI: InChI=1S/C6H8O7/c7-3(8)1-6(13,5(11)12)2-4(9)10/h13H,1-2H2,(H,7,8)(H,9,10)(H,11,12)/p-3
Release date: 2015-02-04