1PLU | Genus

Total Genus 137

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	137
sequence length	352
structure length	352
Chain Sequence	ATDTGGYAATAGGNVTGAVSKTATSMQDIVNIIDAARLDANGKKVKGGAYPLVITYTGNEDSLINAAAANICGQWSKDPRGVEIKEFTKGITIIGANGSSANFGIWIKKSSDVVVQNMRIGYLPGGAKDGDMIRVDDSPNVWVDHNELFAANHECDGTPDNDTTFESAVDIKGASNTVTVSYNYIHGVKKVGLDGSSSSDTGRNITYHHNYYNDVNARLPLQRGGLVHAYNNLYTNITGSGLNVRQNGQALIENNWFEKAINPVTSRYDGKNFGTWVLKGNNITKPADFSTYSITWTADTKPYVNADSWTSTGTFPTVAYNYSPVSAQCVKDKLPGYAGVGKNLATLTSTAC

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

loadScript /static/js/j2s/core/package.js

loadScript /static/js/j2s/core/corejmol.z.js

loadScript /static/js/j2s/core/corescript.z.js

JSmol exec jmolApplet0 start applet null

Jmol JavaScript applet jmolApplet0__711369724586966__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__711369724586966__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/1PLU/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__711369724586966__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"711369724586966","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/1PLU/A/"

Jmol Version: 14.29.13 2018-04-17 17:17

java.vendor: Java2Script (HTML5)

java.version: 2018-01-28 23:38:52 (JSmol/j2s)

os.name: Mozilla/5.0 AppleWebKit/537.36 (KHTML, like Gecko; compatible; ClaudeBot/1.0; +claudebot@anthropic.com)

Access: ALL

memory: 0.0/0.0

processors available: 1

useCommandThread: false

appletId:jmolApplet0 (signed)

Jmol getValue emulate null

defaults = "Jmol"

Jmol getValue boxbgcolor null

Jmol getValue bgcolor white

backgroundColor = "white"

Jmol getValue ANIMFRAMECallback null

Jmol getValue APPLETREADYCallback Jmol._readyCallback

APPLETREADYCallback = "Jmol._readyCallback"

callback set for APPLETREADYCallback Jmol._readyCallback APPLETREADY

Jmol getValue ATOMMOVEDCallback null

Jmol getValue AUDIOCallback null

Jmol getValue CLICKCallback null

Jmol getValue DRAGDROPCallback null

Jmol getValue ECHOCallback null

Jmol getValue ERRORCallback null

Jmol getValue EVALCallback null

Jmol getValue HOVERCallback null

Jmol getValue IMAGECallback null

Jmol getValue LOADSTRUCTCallback null

Jmol getValue MEASURECallback null

Jmol getValue MESSAGECallback null

Jmol getValue MINIMIZATIONCallback null

Jmol getValue SERVICECallback null

Jmol getValue PICKCallback null

Jmol getValue RESIZECallback null

Jmol getValue SCRIPTCallback null

Jmol getValue SYNCCallback null

Jmol getValue STRUCTUREMODIFIEDCallback null

Jmol getValue doTranslate null

language=en_US

Jmol getValue popupMenu null

Jmol getValue script null

Jmol getValue loadInline null

Jmol getValue load null

Jmol applet jmolApplet0__711369724586966__ ready

script 1 started

platformSpeed = 8

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

Genus data interpretation

molecule tags	Lyase
publication title	The Refined Three-Dimensional Structure of Pectate Lyase C from Erwinia chrysanthemi at 2.2 Angstrom Resolution (Implications for an Enzymatic Mechanism). pubmed rcsb
molecule keywords	PROTEIN (PECTATE LYASE C)
total genus	137
structure length	352
sequence length	352
ec nomenclature	ec 4.2.2.2: Pectate lyase.
pdb deposition date	1999-06-04

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF00544	Pec_lyase_C	Pectate lyase

Image from the rcsb pdb (www.rcsb.org)

cath code	Class	Architecture	Topology	Homology	Domain
2.160.20.10	Mainly Beta	3 Solenoid	Pectate Lyase C-like	Single-stranded right-handed beta-helix, Pectin lyase-like	1pluA00

1JTAA 1RWRA 4U49A 4OZZA 2X6WA 3WWGA 2QX3A 4YEJA 2VJJA 3JURA 4PMHA 1O8HA 4XR6A 4XKWA 2QY1A 1K5CA 4I84A 4XNFA 4OJ5A 1KTWA 1O8JA 2UVFA 4OJOA 1CZFA 4XOTA 1QJVA 1O88A 1OGOX 1NHCA 1OGMX 4OJLA 2NT6A 3ZSCA 4XL9A 3GQAA 1OOCA 2X6YA 4YELA 1O8FA 1O8KA 1PXZA 4YZXA 1H80A 1VBLA 4W8SA 2O1DA 3GQ9A 2O04A 2PYGA 3T9GA 4YZ0A 2NTPA 2ODLA 2PECA 1PE9A 3LMWA 3B4NA 1HG8A 3VMWA 1DBOA 4NK8A 1O8EA 4XLFA 5C1CA 4XLHA 3VSVA 5AMVA 4YZQA 1JRGA 2PYHA 4XQFA 1PLUA 2NSPA 1KCDA 3SUCA 3ZPPA 2EWEA 2UVEA 1OFLA 4URRA 2VJIA 4XM3A 2X85A 4XLAA 3FY3A 4AVZA 4HWVA 4XONA 1QCXA 3KRGA 2BSPA 2X6XA 1KCCA 5C1EA 1X0CA 3EQOA 1O8IA 3GRHA 4OJ6A 1IDJA 3GQ8A 4MR0A 4XN3A 4Z05A 4C2LA 1AIRA 3B90A 3VSTA 4OZYA 4W8TA 4XN0A 4Z06A 4XKVA 1EE6A 1OFMA 2VBKA 4XLEA 4XOPA 4U4BA 2QXZA 2X3HA 1RU4A 4XMYA 1GQ8A 4YZAA 1O8LA 2Z8GA 2NZMA 4XLCA 4NK6A 3VMVA 1IDKA 4EW9A 4MXNA 4XORA 2INVA 2O0VA 2VBEA 2INUA 4Z03A 2O0WA 1WMRA 2NSTA 1O8MA 2IQ7A 2NTBA 1RMGA 3GQ7A 1O8GA 3UW0A 2NT9A 1IA5A 2NTQA 2VBMA 3EQNA 4W8RA 3VSUA 1DBGA 3B8YA 1IB4A 4W8QA 4OJPA 1BHEA 1XG2A 2O17A 1BN8A 1O8DA
chains in the Genus database with same CATH superfamily

2V5IA 2XTXA 5JLVC 2O6WA 1JTAA 2J8KA 4YCQA 1RWRA 4U49A 4OZZA 3AK5A 2X6WA 3WWGA 2XT2A 2QX3A 2W7ZA 2QYUA 3TH0A 2BX6A 4YEJA 2XTYA 1LM1A 2VJJA 3JURA 4PMHA 1QA3A 1O8HA 2XC1A 4XR6A 4YEIA 4XKWA 2QY1A 4V02C 3PETA 1K5CA 4I84A 4OM9A 4OJ5A 4XNFA 1KTWA 1O8JA 2UVFA 4OJOA 1LLWA 1KQ5A 1L1IA 1CZFA 3VMVA 1CLWA 4XOTA 1QJVA 1O88A 1OGOX 1NHCA 1TYWA 1OGMX 1QQ1A 4OJLA 2VFQA 3SZEA 2NT6A 3ZSCA 4XL9A 3SYJA 1QRBA 3GQAA 1OOCA 2X6YA 4YFOA 1O8FA 1O8KA 4YELA 1PXZA 4YZXA 2F3LA 1H80A 3PSSA 1VBLA 4W8SA 4YZ0A 2O1DA 1TYXA 3GQ9A 2VFMA 1QA2A 2O04A 2PYGA 2BM6A 2BM4A 4YDTA 3RIQA 3T9GA 2NTPA 1K4ZA 2ODLA 2IOUG 1PE9A 2PECA 3LMWA 3B4NA 1TSPA 2G0YA 1HG8A 3LJYA 3H09A 3VMWA 1DBOA 4NK8A 1O8EA 4XLFA 5C1CA 1EZGA 4XLHA 3VSVA 5AMVA 2VFOA 4YZQA 1JRGA 2PYHA 2VFNA 4XQFA 1PLUA 2NSPA 1KCDA 2XT4A 3SUCA 3ZPPA 2EWEA 1EA0A 2UVEA 3ML3A 1OFLA 4URRA 2VJIA 1HF2A 4XM3A 2X85A 1DABA 4XLAA 3FY3A 4AVZA 4HWVA 4XONA 3PSZA 3LYCA 1QCXA 3KRGA 2BSPA 2X6XA 3DU1X 1KCCA 5C1EA 1X0CA 3EQOA 1O8IA 1K8FA 3GRHA 4OJ6A 1QA1A 1IDJA 3GQ8A 4MR0A 4XN3A 4Z05A 4C2LA 1AIRA 2BM5A 2YUHA 3B90A 2BM7A 3SQVA 3VSTA 4OZYA 4W8TA 4XN0A 2J8IA 4XKVA 4Z06A 1EE6A 1OFMA 2VBKA 4XLEA 4XOPA 3P4GA 2B0RA 3BH7B 4U4BA 2QXZA 1RU4A 2X3HA 4XMYA 1GQ8A 2QZAA 1OFEA 3SY2A 4YZAA 1O8LA 1TYVA 2NZMA 2Z8GA 4NK6A 3NAWA 3NB2A 4XLCA 1IDKA 3N90A 4EW9A 4MXNA 4XORA 2INVA 2O0VA 2VBEA 4OPWA 2INUA 4Z03A 2O0WA 4JRAC 5JMCB 1WXRA 1WMRA 2NSTA 3JX8A 1O8MA 2XTWA 2IQ7A 2NTBA 3BH6B 1RMGA 3GQ7A 1O8GA 3UW0A 2NT9A 1IA5A 1TYUA 2NTQA 2VBMA 2VFPA 3EQNA 1LLZA 4KH3A 4W8RA 5DNSA 1DBGA 3VSUA 1OFDA 3B8YA 3N6ZA 1QRCA 4W8QA 4OJPA 1BHEA 4YC5A 1XG2A 1IB4A 2O17A 1BN8A 1O8DA
chains in the Genus database with same CATH topology

#chains in the Genus database with same CATH superfamily
 1JTA A;  1RWR A;  4U49 A;  4OZZ A;  2X6W A;  3WWG A;  2QX3 A;  4YEJ A;  2VJJ A;  3JUR A;  4PMH A;  1O8H A;  4XR6 A;  4XKW A;  2QY1 A;  1K5C A;  4I84 A;  4XNF A;  4OJ5 A;  1KTW A;  1O8J A;  2UVF A;  4OJO A;  1CZF A;  4XOT A;  1QJV A;  1O88 A;  1OGO X;  1NHC A;  1OGM X;  4OJL A;  2NT6 A;  3ZSC A;  4XL9 A;  3GQA A;  1OOC A;  2X6Y A;  4YEL A;  1O8F A;  1O8K A;  1PXZ A;  4YZX A;  1H80 A;  1VBL A;  4W8S A;  2O1D A;  3GQ9 A;  2O04 A;  2PYG A;  3T9G A;  4YZ0 A;  2NTP A;  2ODL A;  2PEC A;  1PE9 A;  3LMW A;  3B4N A;  1HG8 A;  3VMW A;  1DBO A;  4NK8 A;  1O8E A;  4XLF A;  5C1C A;  4XLH A;  3VSV A;  5AMV A;  4YZQ A;  1JRG A;  2PYH A;  4XQF A;  1PLU A;  2NSP A;  1KCD A;  3SUC A;  3ZPP A;  2EWE A;  2UVE A;  1OFL A;  4URR A;  2VJI A;  4XM3 A;  2X85 A;  4XLA A;  3FY3 A;  4AVZ A;  4HWV A;  4XON A;  1QCX A;  3KRG A;  2BSP A;  2X6X A;  1KCC A;  5C1E A;  1X0C A;  3EQO A;  1O8I A;  3GRH A;  4OJ6 A;  1IDJ A;  3GQ8 A;  4MR0 A;  4XN3 A;  4Z05 A;  4C2L A;  1AIR A;  3B90 A;  3VST A;  4OZY A;  4W8T A;  4XN0 A;  4Z06 A;  4XKV A;  1EE6 A;  1OFM A;  2VBK A;  4XLE A;  4XOP A;  4U4B A;  2QXZ A;  2X3H A;  1RU4 A;  4XMY A;  1GQ8 A;  4YZA A;  1O8L A;  2Z8G A;  2NZM A;  4XLC A;  4NK6 A;  3VMV A;  1IDK A;  4EW9 A;  4MXN A;  4XOR A;  2INV A;  2O0V A;  2VBE A;  2INU A;  4Z03 A;  2O0W A;  1WMR A;  2NST A;  1O8M A;  2IQ7 A;  2NTB A;  1RMG A;  3GQ7 A;  1O8G A;  3UW0 A;  2NT9 A;  1IA5 A;  2NTQ A;  2VBM A;  3EQN A;  4W8R A;  3VSU A;  1DBG A;  3B8Y A;  1IB4 A;  4W8Q A;  4OJP A;  1BHE A;  1XG2 A;  2O17 A;  1BN8 A;  1O8D A; 
#chains in the Genus database with same CATH topology
 2V5I A;  2XTX A;  5JLV C;  2O6W A;  1JTA A;  2J8K A;  4YCQ A;  1RWR A;  4U49 A;  4OZZ A;  3AK5 A;  2X6W A;  3WWG A;  2XT2 A;  2QX3 A;  2W7Z A;  2QYU A;  3TH0 A;  2BX6 A;  4YEJ A;  2XTY A;  1LM1 A;  2VJJ A;  3JUR A;  4PMH A;  1QA3 A;  1O8H A;  2XC1 A;  4XR6 A;  4YEI A;  4XKW A;  2QY1 A;  4V02 C;  3PET A;  1K5C A;  4I84 A;  4OM9 A;  4OJ5 A;  4XNF A;  1KTW A;  1O8J A;  2UVF A;  4OJO A;  1LLW A;  1KQ5 A;  1L1I A;  1CZF A;  3VMV A;  1CLW A;  4XOT A;  1QJV A;  1O88 A;  1OGO X;  1NHC A;  1TYW A;  1OGM X;  1QQ1 A;  4OJL A;  2VFQ A;  3SZE A;  2NT6 A;  3ZSC A;  4XL9 A;  3SYJ A;  1QRB A;  3GQA A;  1OOC A;  2X6Y A;  4YFO A;  1O8F A;  1O8K A;  4YEL A;  1PXZ A;  4YZX A;  2F3L A;  1H80 A;  3PSS A;  1VBL A;  4W8S A;  4YZ0 A;  2O1D A;  1TYX A;  3GQ9 A;  2VFM A;  1QA2 A;  2O04 A;  2PYG A;  2BM6 A;  2BM4 A;  4YDT A;  3RIQ A;  3T9G A;  2NTP A;  1K4Z A;  2ODL A;  2IOU G;  1PE9 A;  2PEC A;  3LMW A;  3B4N A;  1TSP A;  2G0Y A;  1HG8 A;  3LJY A;  3H09 A;  3VMW A;  1DBO A;  4NK8 A;  1O8E A;  4XLF A;  5C1C A;  1EZG A;  4XLH A;  3VSV A;  5AMV A;  2VFO A;  4YZQ A;  1JRG A;  2PYH A;  2VFN A;  4XQF A;  1PLU A;  2NSP A;  1KCD A;  2XT4 A;  3SUC A;  3ZPP A;  2EWE A;  1EA0 A;  2UVE A;  3ML3 A;  1OFL A;  4URR A;  2VJI A;  1HF2 A;  4XM3 A;  2X85 A;  1DAB A;  4XLA A;  3FY3 A;  4AVZ A;  4HWV A;  4XON A;  3PSZ A;  3LYC A;  1QCX A;  3KRG A;  2BSP A;  2X6X A;  3DU1 X;  1KCC A;  5C1E A;  1X0C A;  3EQO A;  1O8I A;  1K8F A;  3GRH A;  4OJ6 A;  1QA1 A;  1IDJ A;  3GQ8 A;  4MR0 A;  4XN3 A;  4Z05 A;  4C2L A;  1AIR A;  2BM5 A;  2YUH A;  3B90 A;  2BM7 A;  3SQV A;  3VST A;  4OZY A;  4W8T A;  4XN0 A;  2J8I A;  4XKV A;  4Z06 A;  1EE6 A;  1OFM A;  2VBK A;  4XLE A;  4XOP A;  3P4G A;  2B0R A;  3BH7 B;  4U4B A;  2QXZ A;  1RU4 A;  2X3H A;  4XMY A;  1GQ8 A;  2QZA A;  1OFE A;  3SY2 A;  4YZA A;  1O8L A;  1TYV A;  2NZM A;  2Z8G A;  4NK6 A;  3NAW A;  3NB2 A;  4XLC A;  1IDK A;  3N90 A;  4EW9 A;  4MXN A;  4XOR A;  2INV A;  2O0V A;  2VBE A;  4OPW A;  2INU A;  4Z03 A;  2O0W A;  4JRA C;  5JMC B;  1WXR A;  1WMR A;  2NST A;  3JX8 A;  1O8M A;  2XTW A;  2IQ7 A;  2NTB A;  3BH6 B;  1RMG A;  3GQ7 A;  1O8G A;  3UW0 A;  2NT9 A;  1IA5 A;  1TYU A;  2NTQ A;  2VBM A;  2VFP A;  3EQN A;  1LLZ A;  4KH3 A;  4W8R A;  5DNS A;  1DBG A;  3VSU A;  1OFD A;  3B8Y A;  3N6Z A;  1QRC A;  4W8Q A;  4OJP A;  1BHE A;  4YC5 A;  1XG2 A;  1IB4 A;  2O17 A;  1BN8 A;  1O8D A; 
#chains in the Genus database with same CATH homology
 1JTA A;  1RWR A;  4U49 A;  4OZZ A;  2X6W A;  3WWG A;  2QX3 A;  4YEJ A;  2VJJ A;  3JUR A;  4PMH A;  1O8H A;  4XR6 A;  4XKW A;  2QY1 A;  1K5C A;  4I84 A;  4XNF A;  4OJ5 A;  1KTW A;  1O8J A;  2UVF A;  4OJO A;  1CZF A;  4XOT A;  1QJV A;  1O88 A;  1OGO X;  1NHC A;  1OGM X;  4OJL A;  2NT6 A;  3ZSC A;  4XL9 A;  3GQA A;  1OOC A;  2X6Y A;  4YEL A;  1O8F A;  1O8K A;  1PXZ A;  4YZX A;  1H80 A;  1VBL A;  4W8S A;  2O1D A;  3GQ9 A;  2O04 A;  2PYG A;  3T9G A;  4YZ0 A;  2NTP A;  2ODL A;  2PEC A;  1PE9 A;  3LMW A;  3B4N A;  1HG8 A;  3VMW A;  1DBO A;  4NK8 A;  1O8E A;  4XLF A;  5C1C A;  4XLH A;  3VSV A;  5AMV A;  4YZQ A;  1JRG A;  2PYH A;  4XQF A;  1PLU A;  2NSP A;  1KCD A;  3SUC A;  3ZPP A;  2EWE A;  2UVE A;  1OFL A;  4URR A;  2VJI A;  4XM3 A;  2X85 A;  4XLA A;  3FY3 A;  4AVZ A;  4HWV A;  4XON A;  1QCX A;  3KRG A;  2BSP A;  2X6X A;  1KCC A;  5C1E A;  1X0C A;  3EQO A;  1O8I A;  3GRH A;  4OJ6 A;  1IDJ A;  3GQ8 A;  4MR0 A;  4XN3 A;  4Z05 A;  4C2L A;  1AIR A;  3B90 A;  3VST A;  4OZY A;  4W8T A;  4XN0 A;  4Z06 A;  4XKV A;  1EE6 A;  1OFM A;  2VBK A;  4XLE A;  4XOP A;  4U4B A;  2QXZ A;  2X3H A;  1RU4 A;  4XMY A;  1GQ8 A;  4YZA A;  1O8L A;  2Z8G A;  2NZM A;  4XLC A;  4NK6 A;  3VMV A;  1IDK A;  4EW9 A;  4MXN A;  4XOR A;  2INV A;  2O0V A;  2VBE A;  2INU A;  4Z03 A;  2O0W A;  1WMR A;  2NST A;  1O8M A;  2IQ7 A;  2NTB A;  1RMG A;  3GQ7 A;  1O8G A;  3UW0 A;  2NT9 A;  1IA5 A;  2NTQ A;  2VBM A;  3EQN A;  4W8R A;  3VSU A;  1DBG A;  3B8Y A;  1IB4 A;  4W8Q A;  4OJP A;  1BHE A;  1XG2 A;  2O17 A;  1BN8 A;  1O8D A;

...loading similar chains, please wait...
similar chains in the Genus database (?% sequence similarity)

...loading similar chains, please wait...
similar chains in the pdb database (?% sequence similarity)

#similar chains in the Genus database (?% sequence similarity)
...loading similar chains, please wait...
#similar chains, but unknotted
...loading similar chains, please wait...
#similar chains in the pdb database (?% sequence similarity)
...loading similar chains, please wait...

1PLUA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

pfam database annotations