1O88 | Genus

Total Genus 141

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	141
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

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Viewer cachePut cache://localLOAD_/file/5cfbb5d02d5d85c0cbfb4baa/pdb.gz

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The Resolver thinks Pdb

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

Time for openFile(/file/5cfbb5d02d5d85c0cbfb4baa/pdb.gz): 1437 ms

reading 352 atoms

ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false

1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.

Default Van der Waals type for model set to Jmol

352 atoms created

ModelSet: autobonding; use autobond=false to not generate bonds automatically

Time for creating model: 26 ms

Adding embedded #jmolscript: select ({0:351});backbone only;select *;

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	Hydrolase
source organism	Erwinia chrysanthemi
publication title	Characterization and Implications of Ca2+ Binding to Pectate Lyase C pubmed doi rcsb
molecule keywords	PECTATE LYASE C
total genus	141
structure length	352
sequence length	352
ec nomenclature	ec 4.2.2.2: Pectate lyase.
pdb deposition date	2002-11-26

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	1o88A00

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

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

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

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similar chains in the Genus database (?% sequence similarity)

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#similar chains in the Genus database (?% sequence similarity)
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#similar chains, but unknotted
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1O88A

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

pfam database annotations