2OTN | Genus

Total Genus 65

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	65
sequence length	293
structure length	293
Chain Sequence	VPRGSHMSQFSFTKMHGLGNSYIYVNMFEEQIPEEDLALVAEKVSNINTGIGADGMILICPSDVAPVKMRMFNNDGSEGKSCGNGLRCVAKYAYEHKLVEDTVFTIETLAGIVTAEVTVEEGKVTLAKIDMGAPRLTRAEIPMLGEGETPFIRENFLYNNHRYAFTAVSMGNPHAVIFVDDVEQAPLTTLGPVLETHEMFPERVNVEFIEILNEEEMNFRVWERGSGVTQACGTGACAAVVASILNGKMERGKEITVHLAGGDLMIAWTEEGNVLMKGPAEVICRGVYEYKIE

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/5cfd6679d84f7d86633eb43b/pdb.gz

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The Resolver thinks Pdb

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Time for openFile(/file/5cfd6679d84f7d86633eb43b/pdb.gz): 1090 ms

reading 293 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

293 atoms created

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

Time for creating model: 28 ms

Adding embedded #jmolscript: select ({0:292});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	Isomerase
source organism	Bacillus anthracis str.
publication title	Crystal structure and inhibition of a catalytically active form of diaminopimelate epimerase (DapF)from Bacillus anthracis rcsb
molecule keywords	Diaminopimelate epimerase
total genus	65
structure length	293
sequence length	293
chains with identical sequence	B
ec nomenclature	ec 5.1.1.7: Diaminopimelate epimerase.
pdb deposition date	2007-02-08

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF01678	DAP_epimerase	Diaminopimelate epimerase

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

cath code	Class	Architecture	Topology	Homology	Domain
3.10.310.10	Alpha Beta	Roll	Diaminopimelate Epimerase; Chain A, domain 1	Diaminopimelate Epimerase; Chain A, domain 1	2otnA02
3.10.310.10	Alpha Beta	Roll	Diaminopimelate Epimerase; Chain A, domain 1	Diaminopimelate Epimerase; Chain A, domain 1	2otnA01

5H2YA 2GKEA 4J9XA 4J9WA 2OTNA 4Q2HA 5HA4A 3EDNA 1W61A 1QY9A 2AZPA 4JBDA 5M47A 2PW0A 1QYAA 1U1VA 1SDJA 1S7JA 1BWZA 1T6KA 1GQZA 2PVZA 4IJZA 3EKMA 4IK0A 4JUUA 1U1WA 2Q9HA 4K7GB 4JCIA 5H2GA 5IWEA 1U1XA 4K7XA 4K8LA 1YM5A 2H9FA 3FVEA 4Q60A 2Q9JA 1XUBA 4JD7A 1W62A 4LB0A 1XUAA 4DUNA 3G7KA 2GKJA 1U0KA 1TM0A 3EJXA
chains in the Genus database with same CATH superfamily

5H2YA 2EB0A 4LG3A 2ZXRA 1IR6A 3IGHX 4GL6A 1U1VA 4PY9A 1WPMA 2ZXPA 1T6KA 1GQZA 2ZXOA 2KPTA 3WQZA 1I74A 1YM5A 3PW9A 1XUAA 2YMAA 4IJZA 4J9WA 3EDNA 3W5WA 4RPAA 1SDJA 1K23A 2KW7A 1K20A 2PVZA 2HAWA 3EKMA 2QB8A 2QB6A 1U1WA 2IW4A 3G98A 4K7GB 5H2GA 2MPBA 1U1XA 2Q9JA 1XUBA 3PVHA 4DUNA 2GKJA 1U0KA 2GKEA 2OTNA 5HA4A 1W61A 1QY9A 2AZPA 4JBDA 3ICJA 1QYAA 2LT2A 2ZVFA 2QB7A 1BWZA 4IK0A 4JUUA 3PTJA 2Q9HA 4JCIA 5IWEA 4OA3A 2H9FA 3FVEA 4LB0A 1W62A 1WPPA 3G7KA 1TM0A 3EJXA 4J9XA 4Q2HA 5M47A 3DEVA 2PW0A 4LS9A 2ENXA 1S7JA 5ANPA 4K7XA 4K8LA 4Q60A 4JD7A
chains in the Genus database with same CATH topology

#chains in the Genus database with same CATH superfamily
 5H2Y A;  2GKE A;  4J9X A;  4J9W A;  2OTN A;  4Q2H A;  5HA4 A;  3EDN A;  1W61 A;  1QY9 A;  2AZP A;  4JBD A;  5M47 A;  2PW0 A;  1QYA A;  1U1V A;  1SDJ A;  1S7J A;  1BWZ A;  1T6K A;  1GQZ A;  2PVZ A;  4IJZ A;  3EKM A;  4IK0 A;  4JUU A;  1U1W A;  2Q9H A;  4K7G B;  4JCI A;  5H2G A;  5IWE A;  1U1X A;  4K7X A;  4K8L A;  1YM5 A;  2H9F A;  3FVE A;  4Q60 A;  2Q9J A;  1XUB A;  4JD7 A;  1W62 A;  4LB0 A;  1XUA A;  4DUN A;  3G7K A;  2GKJ A;  1U0K A;  1TM0 A;  3EJX A; 
#chains in the Genus database with same CATH topology
 5H2Y A;  2EB0 A;  4LG3 A;  2ZXR A;  1IR6 A;  3IGH X;  4GL6 A;  1U1V A;  4PY9 A;  1WPM A;  2ZXP A;  1T6K A;  1GQZ A;  2ZXO A;  2KPT A;  3WQZ A;  1I74 A;  1YM5 A;  3PW9 A;  1XUA A;  2YMA A;  4IJZ A;  4J9W A;  3EDN A;  3W5W A;  4RPA A;  1SDJ A;  1K23 A;  2KW7 A;  1K20 A;  2PVZ A;  2HAW A;  3EKM A;  2QB8 A;  2QB6 A;  1U1W A;  2IW4 A;  3G98 A;  4K7G B;  5H2G A;  2MPB A;  1U1X A;  2Q9J A;  1XUB A;  3PVH A;  4DUN A;  2GKJ A;  1U0K A;  2GKE A;  2OTN A;  5HA4 A;  1W61 A;  1QY9 A;  2AZP A;  4JBD A;  3ICJ A;  1QYA A;  2LT2 A;  2ZVF A;  2QB7 A;  1BWZ A;  4IK0 A;  4JUU A;  3PTJ A;  2Q9H A;  4JCI A;  5IWE A;  4OA3 A;  2H9F A;  3FVE A;  4LB0 A;  1W62 A;  1WPP A;  3G7K A;  1TM0 A;  3EJX A;  4J9X A;  4Q2H A;  5M47 A;  3DEV A;  2PW0 A;  4LS9 A;  2ENX A;  1S7J A;  5ANP A;  4K7X A;  4K8L A;  4Q60 A;  4JD7 A; 
#chains in the Genus database with same CATH homology
 5H2Y A;  2EB0 A;  4LG3 A;  2ZXR A;  1IR6 A;  3IGH X;  4GL6 A;  1U1V A;  4PY9 A;  1WPM A;  2ZXP A;  1T6K A;  1GQZ A;  2ZXO A;  2KPT A;  3WQZ A;  1I74 A;  1YM5 A;  3PW9 A;  1XUA A;  2YMA A;  4IJZ A;  4J9W A;  3EDN A;  3W5W A;  4RPA A;  1SDJ A;  1K23 A;  2KW7 A;  1K20 A;  2PVZ A;  2HAW A;  3EKM A;  2QB8 A;  2QB6 A;  1U1W A;  2IW4 A;  3G98 A;  4K7G B;  5H2G A;  2MPB A;  1U1X A;  2Q9J A;  1XUB A;  3PVH A;  4DUN A;  2GKJ A;  1U0K A;  2GKE A;  2OTN A;  5HA4 A;  1W61 A;  1QY9 A;  2AZP A;  4JBD A;  3ICJ A;  1QYA A;  2LT2 A;  2ZVF A;  2QB7 A;  1BWZ A;  4IK0 A;  4JUU A;  3PTJ A;  2Q9H A;  4JCI A;  5IWE A;  4OA3 A;  2H9F A;  3FVE A;  4LB0 A;  1W62 A;  1WPP A;  3G7K A;  1TM0 A;  3EJX A;  4J9X A;  4Q2H A;  5M47 A;  3DEV A;  2PW0 A;  4LS9 A;  2ENX A;  1S7J A;  5ANP A;  4K7X A;  4K8L A;  4Q60 A;  4JD7 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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#similar chains in the pdb database (?% sequence similarity)
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2OTNA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations