1YMDA

Crystal structure of the cdc25b phosphatase catalytic domain with the active site cysteine in the sulfonic form
Total Genus 58
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The genus trace: a function that shows values of genus (vertical axis) for subchains spanned between the first residue, and all other residues (shown on horizontal axis). The number of the latter residue and the genus of a given subchain are shown interactively.

Total Genus
58
sequence length
175
structure length
170
Chain Sequence
MELIGDYSKAFLLQTVDGKHQDLKYISPETMVALLTGKFSNIVDKFVIVDCRYPYEYEGGHIKTAVNLPLERDAESFLLKSPIAPKRVILIFHEFSSERGPRMCRFIRERDRAVNDYPSLYYPEMYILKGGYKEFFPQHPNFCEPQDYRPMNHEAFKDELKTFRLKTRSW
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The genus matrix. At position (x,y) a genus value for a subchain spanned between x’th and y’th residue is shown. Values of the genus are represented by color, according to the scale given on the right.

Structure visualization

After clicking on a point (x,y) in the genus matrix above, a subchain from x to y is shown in color.

molecule tags Hydrolase, cell cycle
molecule keywords M-phase inducer phosphatase 2
publication title Structural Mechanism of Oxidative Regulation of the Phosphatase Cdc25B via an Intramolecular Disulfide Bond
pubmed doi rcsb
source organism Homo sapiens
total genus 58
structure length 170
sequence length 175
ec nomenclature ec 3.1.3.48: Protein-tyrosine-phosphatase.
pdb deposition date 2005-01-20

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF00581 Rhodanese Rhodanese-like domain
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
3.40.250.10 Alpha Beta 3-Layer(aba) Sandwich Oxidized Rhodanese; domain 1 Rhodanese-like domain 1ymdA00
3AAYA 1YT8A 5HPAA 2VSWA 3I3UA 1C25A 2FSXA 4WH7A 3R2UA 2JTQA 2WLXA 3HWIA 5HBLA 1CWTA 3I2VA 3TG1B 1WV9A 3NT6A 3NHVA 5HBPA 2HHGA 5HBQA 3OP3A 2OUCA 3IPOA 5LAMA 2ORAA 2IFDA 2WLRA 1H4KX 1TQ1A 3FOJA 1BOHA 2UZQA 1DP2A 3HZUA 1YMKA 1BOIA 3F4AA 2EG4A 3FS5A 4OCGA 3TG3A 2EG3A 2JTRA 3HIXA 1VEEA 4F67A 3IWHA 1URHA 3NTDA 3TP9A 5HBOA 1CWRA 1HZMA 3ICSA 2MOLA 1GMXA 3K9RA 2KL3A 1UARA 1CWSA 1H4MX 3FLHA 1OKGA 3ILMA 3P3AA 2J6PA 3ICTA 3GK5A 3D1PA 2DCQA 3FNJA 2MOIA 1YS0A 3OLHA 5LAOA 2GWFA 1WHBA 1T3KA 1ORBA 2EG4B 4JGTA 3MZZA 2K0ZA 2A2KA 2JTSA 2MRMA 1YMDA 3IPPA 3AAXA 2IFVA 4WH9A 1GN0A 1QB0A 3ICRA 1E0CA 1YMLA 3G5JA 1RHDA 1RHSA 1QXNA 3UTNX 3O3WA 1YM9A 3NTAA
chains in the Genus database with same CATH superfamily
3AAYA 1YT8A 5HPAA 2VSWA 3I3UA 1C25A 2FSXA 4WH7A 3R2UA 2JTQA 2WLXA 3HWIA 5HBLA 1CWTA 3I2VA 3TG1B 1WV9A 3NT6A 3NHVA 5HBPA 2HHGA 5HBQA 3OP3A 2OUCA 3IPOA 5LAMA 2ORAA 2IFDA 2WLRA 1H4KX 1TQ1A 3FOJA 1BOHA 2UZQA 1DP2A 3HZUA 1YMKA 1BOIA 3F4AA 2EG4A 3FS5A 4OCGA 3TG3A 2EG3A 2JTRA 3HIXA 1VEEA 4F67A 3IWHA 1URHA 3NTDA 3TP9A 5HBOA 1CWRA 1HZMA 3ICSA 2MOLA 1GMXA 3K9RA 2KL3A 1UARA 1CWSA 1H4MX 3FLHA 1OKGA 3ILMA 3P3AA 2J6PA 3ICTA 3GK5A 3D1PA 2DCQA 3FNJA 2MOIA 1YS0A 3OLHA 5LAOA 2GWFA 1WHBA 2Q82A 1T3KA 1ORBA 2EG4B 4JGTA 3MZZA 2K0ZA 2A2KA 2JTSA 2MRMA 1YMDA 3IPPA 3AAXA 2IFVA 4WH9A 1GN0A 1QB0A 3ICRA 1E0CA 1YMLA 3G5JA 1RHDA 1RHSA 1QXNA 3UTNX 3O3WA 1YM9A 3NTAA
chains in the Genus database with same CATH topology
3AAYA 1YT8A 5HPAA 2VSWA 3I3UA 1C25A 2FSXA 4WH7A 3R2UA 2JTQA 2WLXA 3HWIA 5HBLA 1CWTA 3I2VA 3TG1B 1WV9A 3NT6A 3NHVA 5HBPA 2HHGA 5HBQA 3OP3A 2OUCA 3IPOA 5LAMA 2ORAA 2IFDA 2WLRA 1H4KX 1TQ1A 3FOJA 1BOHA 2UZQA 1DP2A 3HZUA 1YMKA 1BOIA 3F4AA 2EG4A 3FS5A 4OCGA 3TG3A 2EG3A 2JTRA 3HIXA 1VEEA 4F67A 3IWHA 1URHA 3NTDA 3TP9A 5HBOA 1CWRA 1HZMA 3ICSA 2MOLA 1GMXA 3K9RA 2KL3A 1UARA 1CWSA 1H4MX 3FLHA 1OKGA 3ILMA 3P3AA 2J6PA 3ICTA 3GK5A 3D1PA 2DCQA 3FNJA 2MOIA 1YS0A 3OLHA 5LAOA 2GWFA 1WHBA 1T3KA 1ORBA 2EG4B 4JGTA 3MZZA 2K0ZA 2A2KA 2JTSA 2MRMA 1YMDA 3IPPA 3AAXA 2IFVA 4WH9A 1GN0A 1QB0A 3ICRA 1E0CA 1YMLA 3G5JA 1RHDA 1RHSA 1QXNA 3UTNX 3O3WA 1YM9A 3NTAA
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 3AAY A;  1YT8 A;  5HPA A;  2VSW A;  3I3U A;  1C25 A;  2FSX A;  4WH7 A;  3R2U A;  2JTQ A;  2WLX A;  3HWI A;  5HBL A;  1CWT A;  3I2V A;  3TG1 B;  1WV9 A;  3NT6 A;  3NHV A;  5HBP A;  2HHG A;  5HBQ A;  3OP3 A;  2OUC A;  3IPO A;  5LAM A;  2ORA A;  2IFD A;  2WLR A;  1H4K X;  1TQ1 A;  3FOJ A;  1BOH A;  2UZQ A;  1DP2 A;  3HZU A;  1YMK A;  1BOI A;  3F4A A;  2EG4 A;  3FS5 A;  4OCG A;  3TG3 A;  2EG3 A;  2JTR A;  3HIX A;  1VEE A;  4F67 A;  3IWH A;  1URH A;  3NTD A;  3TP9 A;  5HBO A;  1CWR A;  1HZM A;  3ICS A;  2MOL A;  1GMX A;  3K9R A;  2KL3 A;  1UAR A;  1CWS A;  1H4M X;  3FLH A;  1OKG A;  3ILM A;  3P3A A;  2J6P A;  3ICT A;  3GK5 A;  3D1P A;  2DCQ A;  3FNJ A;  2MOI A;  1YS0 A;  3OLH A;  5LAO A;  2GWF A;  1WHB A;  1T3K A;  1ORB A;  2EG4 B;  4JGT A;  3MZZ A;  2K0Z A;  2A2K A;  2JTS A;  2MRM A;  1YMD A;  3IPP A;  3AAX A;  2IFV A;  4WH9 A;  1GN0 A;  1QB0 A;  3ICR A;  1E0C A;  1YML A;  3G5J A;  1RHD A;  1RHS A;  1QXN A;  3UTN X;  3O3W A;  1YM9 A;  3NTA A; 
#chains in the Genus database with same CATH topology
 3AAY A;  1YT8 A;  5HPA A;  2VSW A;  3I3U A;  1C25 A;  2FSX A;  4WH7 A;  3R2U A;  2JTQ A;  2WLX A;  3HWI A;  5HBL A;  1CWT A;  3I2V A;  3TG1 B;  1WV9 A;  3NT6 A;  3NHV A;  5HBP A;  2HHG A;  5HBQ A;  3OP3 A;  2OUC A;  3IPO A;  5LAM A;  2ORA A;  2IFD A;  2WLR A;  1H4K X;  1TQ1 A;  3FOJ A;  1BOH A;  2UZQ A;  1DP2 A;  3HZU A;  1YMK A;  1BOI A;  3F4A A;  2EG4 A;  3FS5 A;  4OCG A;  3TG3 A;  2EG3 A;  2JTR A;  3HIX A;  1VEE A;  4F67 A;  3IWH A;  1URH A;  3NTD A;  3TP9 A;  5HBO A;  1CWR A;  1HZM A;  3ICS A;  2MOL A;  1GMX A;  3K9R A;  2KL3 A;  1UAR A;  1CWS A;  1H4M X;  3FLH A;  1OKG A;  3ILM A;  3P3A A;  2J6P A;  3ICT A;  3GK5 A;  3D1P A;  2DCQ A;  3FNJ A;  2MOI A;  1YS0 A;  3OLH A;  5LAO A;  2GWF A;  1WHB A;  2Q82 A;  1T3K A;  1ORB A;  2EG4 B;  4JGT A;  3MZZ A;  2K0Z A;  2A2K A;  2JTS A;  2MRM A;  1YMD A;  3IPP A;  3AAX A;  2IFV A;  4WH9 A;  1GN0 A;  1QB0 A;  3ICR A;  1E0C A;  1YML A;  3G5J A;  1RHD A;  1RHS A;  1QXN A;  3UTN X;  3O3W A;  1YM9 A;  3NTA A; 
#chains in the Genus database with same CATH homology
 3AAY A;  1YT8 A;  5HPA A;  2VSW A;  3I3U A;  1C25 A;  2FSX A;  4WH7 A;  3R2U A;  2JTQ A;  2WLX A;  3HWI A;  5HBL A;  1CWT A;  3I2V A;  3TG1 B;  1WV9 A;  3NT6 A;  3NHV A;  5HBP A;  2HHG A;  5HBQ A;  3OP3 A;  2OUC A;  3IPO A;  5LAM A;  2ORA A;  2IFD A;  2WLR A;  1H4K X;  1TQ1 A;  3FOJ A;  1BOH A;  2UZQ A;  1DP2 A;  3HZU A;  1YMK A;  1BOI A;  3F4A A;  2EG4 A;  3FS5 A;  4OCG A;  3TG3 A;  2EG3 A;  2JTR A;  3HIX A;  1VEE A;  4F67 A;  3IWH A;  1URH A;  3NTD A;  3TP9 A;  5HBO A;  1CWR A;  1HZM A;  3ICS A;  2MOL A;  1GMX A;  3K9R A;  2KL3 A;  1UAR A;  1CWS A;  1H4M X;  3FLH A;  1OKG A;  3ILM A;  3P3A A;  2J6P A;  3ICT A;  3GK5 A;  3D1P A;  2DCQ A;  3FNJ A;  2MOI A;  1YS0 A;  3OLH A;  5LAO A;  2GWF A;  1WHB A;  1T3K A;  1ORB A;  2EG4 B;  4JGT A;  3MZZ A;  2K0Z A;  2A2K A;  2JTS A;  2MRM A;  1YMD A;  3IPP A;  3AAX A;  2IFV A;  4WH9 A;  1GN0 A;  1QB0 A;  3ICR A;  1E0C A;  1YML A;  3G5J A;  1RHD A;  1RHS A;  1QXN A;  3UTN X;  3O3W A;  1YM9 A;  3NTA A; 
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similar chains in the Genus database (?% sequence similarity)
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similar chains in the pdb database (?% sequence similarity)

 
#similar chains in the Genus database (?% sequence similarity)
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#similar chains, but unknotted
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