3PVJ | Genus

Total Genus 83

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	83
sequence length	275
structure length	275
Chain Sequence	LTITPLSPALGAQISGVDISRDISAEERDAIEQALLQHQVLFLRDQPINPEQQARFAARFGDLHIHPIYPNVPDTPQVLVLDTAVTDVRDNAVWHTDVTFLPTPALGAVLSAKQLPAYGGDTLWASGIAAFEALSAPLREMLDGLTATHDFTKSFPLERFGTTPQDLARWEATRRNNPPLSHPVVRTHPVSGRKALFVNEGFTTRINELSELESDALLRLLFAHATRPEFSIRWRWQENDVAFWDNRVTQHFAVDDYRPNRRVMHRATILGDAPF

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/5cffe78ce725ee1fe4aa2f57/pdb.gz

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The Resolver thinks Pdb

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Time for openFile(/file/5cffe78ce725ee1fe4aa2f57/pdb.gz): 1669 ms

reading 275 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

275 atoms created

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

Time for creating model: 24 ms

Adding embedded #jmolscript: select ({0:274});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

Chord Diagram

molecule tags	Oxidoreductase
source organism	Pseudomonas putida kt2440
publication title	Biochemical and structural characterization of the Fe(II)/alpha-ketoglutarate dependent taurine dioxygenase from Pseudomonas putida KT2440 rcsb
molecule keywords	Alpha-ketoglutarate-dependent taurine dioxygenase
total genus	83
structure length	275
sequence length	275
chains with identical sequence	B, C, D
ec nomenclature	ec 1.14.11.17: Taurine dioxygenase.
pdb deposition date	2010-12-07

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF02668	TauD	Taurine catabolism dioxygenase TauD, TfdA family

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

cath code	Class	Architecture	Topology	Homology	Domain
3.60.130.10	Alpha Beta	4-Layer Sandwich	Double-stranded beta-helix	Clavaminate synthase-like	3pvjA00

4BHGA 1GY9A 1VZ4A 1OTJA 1OIHA 1OIIA 4M2EA 5J92A 4M26A 4BHIA 4Y0EA 1DRYA 1Y0ZA 4BGMA 4M2FA 1OS7A 2OG6A 2WBQA 1GQWA 2OG7A 4J5IA 1GVGA 4M2GA 4YLMX 4C8RA 1OIJB 4M25A 4FFAA 4CWDA 1DS1A 3PVJA 2Q4AA 4M2IA 4OJ8A 1OIJC 4M23A 3R1JA 5HSXA 4CVYA 3MS5A 1NX4A 3EATX 2WBOA 4NE0A 3V17A 4BHFA 3V15A 4M27A 1JR7A 3O2GA 4C5WA 1OIJA 4BGKA 1DRTA 1OIKA 5KEUA 1NX8A 4M2CA 3SWTA 2WBPA 1VZ5A 1DS0A 4BG1A 2OG5A 2R6SA 3N6WA
chains in the Genus database with same CATH superfamily

4BHGA 1GY9A 1VZ4A 1OTJA 1OIHA 1OIIA 4M2EA 5J92A 4M26A 4BHIA 4Y0EA 1DRYA 1Y0ZA 4BGMA 4M2FA 1OS7A 2OG6A 2WBQA 1GQWA 2OG7A 4J5IA 1GVGA 4M2GA 4YLMX 4C8RA 1OIJB 4M25A 1PG6A 4FFAA 4CWDA 1DS1A 3PVJA 2Q4AA 4M2IA 4OJ8A 1OIJC 4M23A 3R1JA 5HSXA 4CVYA 3MS5A 1NX4A 3EATX 2WBOA 4NE0A 3V17A 4BHFA 3V15A 4M27A 1JR7A 1YOXA 3O2GA 4C5WA 1OIJA 4BGKA 1DRTA 1OIKA 5KEUA 1NX8A 4M2CA 3SWTA 2WBPA 1VZ5A 1DS0A 4BG1A 2OG5A 2R6SA 3N6WA
chains in the Genus database with same CATH topology

1GY9A 1H2MA 4NR1A 4M26A 1DRYA 4BGMA 2OG6A 2WBQA 1GQWA 2OG7A 4J5IA 4YLMX 3P3NA 1OIJB 1H2NA 1DS1A 2Q4AA 1H2LA 2W0XA 1YCIA 4OJ8A 4M23A 1IZ3A 1NX4A 3V17A 4BHFA 1MZFA 5KEUA 1NX8A 4M2CA 3SWTA 1DS0A 2ILMA 3N6WA 4BHGA 1H2KA 4BIOA 1OS7A 1GVGA 4M2GA 5JWPA 4FFAA 3PVJA 3R1JA 4CVYA 3MS5A 3EATX 2WBOA 3V15A 4M27A 1JR7A 2WA3A 3D8CA 1OIJA 4Z1VA 4AI8A 1VZ5A 3KCXA 1VZ4A 1OIIA 5J92A 2YC0A 4Y0EA 1Y0ZA 4M2FA 4C8RA 4CWDA 4M2IA 4B7KA 2CGNA 3P3PA 4NE0A 4JAAA 3O2GA 4C5WA 4BGKA 1DRTA 2Y0IA 2CGOA 2OG5A 1OTJA 1OIHA 4B7EA 4M2EA 4BHIA 2WA4A 2XUMA 2YDEA 4M25A 1MZEA 4Z2WA 1OIJC 5HSXA 1OIKA 2WBPA 4BG1A 3KCYA 2R6SA 3OD4A
chains in the Genus database with same CATH homology

#chains in the Genus database with same CATH superfamily
 4BHG A;  1GY9 A;  1VZ4 A;  1OTJ A;  1OIH A;  1OII A;  4M2E A;  5J92 A;  4M26 A;  4BHI A;  4Y0E A;  1DRY A;  1Y0Z A;  4BGM A;  4M2F A;  1OS7 A;  2OG6 A;  2WBQ A;  1GQW A;  2OG7 A;  4J5I A;  1GVG A;  4M2G A;  4YLM X;  4C8R A;  1OIJ B;  4M25 A;  4FFA A;  4CWD A;  1DS1 A;  3PVJ A;  2Q4A A;  4M2I A;  4OJ8 A;  1OIJ C;  4M23 A;  3R1J A;  5HSX A;  4CVY A;  3MS5 A;  1NX4 A;  3EAT X;  2WBO A;  4NE0 A;  3V17 A;  4BHF A;  3V15 A;  4M27 A;  1JR7 A;  3O2G A;  4C5W A;  1OIJ A;  4BGK A;  1DRT A;  1OIK A;  5KEU A;  1NX8 A;  4M2C A;  3SWT A;  2WBP A;  1VZ5 A;  1DS0 A;  4BG1 A;  2OG5 A;  2R6S A;  3N6W A; 
#chains in the Genus database with same CATH topology
 4BHG A;  1GY9 A;  1VZ4 A;  1OTJ A;  1OIH A;  1OII A;  4M2E A;  5J92 A;  4M26 A;  4BHI A;  4Y0E A;  1DRY A;  1Y0Z A;  4BGM A;  4M2F A;  1OS7 A;  2OG6 A;  2WBQ A;  1GQW A;  2OG7 A;  4J5I A;  1GVG A;  4M2G A;  4YLM X;  4C8R A;  1OIJ B;  4M25 A;  1PG6 A;  4FFA A;  4CWD A;  1DS1 A;  3PVJ A;  2Q4A A;  4M2I A;  4OJ8 A;  1OIJ C;  4M23 A;  3R1J A;  5HSX A;  4CVY A;  3MS5 A;  1NX4 A;  3EAT X;  2WBO A;  4NE0 A;  3V17 A;  4BHF A;  3V15 A;  4M27 A;  1JR7 A;  1YOX A;  3O2G A;  4C5W A;  1OIJ A;  4BGK A;  1DRT A;  1OIK A;  5KEU A;  1NX8 A;  4M2C A;  3SWT A;  2WBP A;  1VZ5 A;  1DS0 A;  4BG1 A;  2OG5 A;  2R6S A;  3N6W A; 
#chains in the Genus database with same CATH homology
 1GY9 A;  1H2M A;  4NR1 A;  4M26 A;  1DRY A;  4BGM A;  2OG6 A;  2WBQ A;  1GQW A;  2OG7 A;  4J5I A;  4YLM X;  3P3N A;  1OIJ B;  1H2N A;  1DS1 A;  2Q4A A;  1H2L A;  2W0X A;  1YCI A;  4OJ8 A;  4M23 A;  1IZ3 A;  1NX4 A;  3V17 A;  4BHF A;  1MZF A;  5KEU A;  1NX8 A;  4M2C A;  3SWT A;  1DS0 A;  2ILM A;  3N6W A;  4BHG A;  1H2K A;  4BIO A;  1OS7 A;  1GVG A;  4M2G A;  5JWP A;  4FFA A;  3PVJ A;  3R1J A;  4CVY A;  3MS5 A;  3EAT X;  2WBO A;  3V15 A;  4M27 A;  1JR7 A;  2WA3 A;  3D8C A;  1OIJ A;  4Z1V A;  4AI8 A;  1VZ5 A;  3KCX A;  1VZ4 A;  1OII A;  5J92 A;  2YC0 A;  4Y0E A;  1Y0Z A;  4M2F A;  4C8R A;  4CWD A;  4M2I A;  4B7K A;  2CGN A;  3P3P A;  4NE0 A;  4JAA A;  3O2G A;  4C5W A;  4BGK A;  1DRT A;  2Y0I A;  2CGO A;  2OG5 A;  1OTJ A;  1OIH A;  4B7E A;  4M2E A;  4BHI A;  2WA4 A;  2XUM A;  2YDE A;  4M25 A;  1MZE A;  4Z2W A;  1OIJ C;  5HSX A;  1OIK A;  2WBP A;  4BG1 A;  3KCY A;  2R6S A;  3OD4 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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3PVJA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations