2H7G | Genus

Total Genus 91

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	91
sequence length	312
structure length	312
Chain Sequence	MRALFYKDGKLFTDNNFLNPVSDNNPAYEVLQHVKIPTHLTDVVVYGQTWEEALTRLIFVGSDSKGRRQYFYGKMHVQNRNAKRDRIFVRVYNVMKRINSFINKNIKKSSTDSNYQLAVFMLMETMFFIRFGKMKYLKENETVGLLTLKNKHIEISPDKIVIKFVGKDKVSHEFVVHKSNRLYKPLLKLTDDSSPEEFLFNKLSERKVYESIKQFGIRIKDLRTYGVNYTFLYNFWTNVKSISPLPSPKKLIALTIKQTAEVVGHTPSISKRAYMATTILEMVKDKNFLDVVSKTTFDEFLSIVVDHVKSST

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/5d2529f21b2a4bad519b9353/pdb.gz

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The Resolver thinks Pdb

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

Time for openFile(/file/5d2529f21b2a4bad519b9353/pdb.gz): 1309 ms

reading 312 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

312 atoms created

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

Time for creating model: 27 ms

Adding embedded #jmolscript: select ({0:311});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/dna
source organism	Variola virus
publication title	Structural basis for specificity in the poxvirus topoisomerase. pubmed doi rcsb
molecule keywords	5'-D(TPTPGPTPCPGPCPCPCPTPTPA)-3'
total genus	91
structure length	312
sequence length	312
ec nomenclature	ec 5.99.1.2: Transferred entry: 5.6.2.2.
pdb deposition date	2006-06-02

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
X	PF01028	Topoisom_I	Eukaryotic DNA topoisomerase I, catalytic core
X	PF09266	VirDNA-topo-I_N	Viral DNA topoisomerase I, N-terminal

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

cath code	Class	Architecture	Topology	Homology	Domain
3.30.66.10	Alpha Beta	2-Layer Sandwich	Viral Topoisomerase I	DNA topoisomerase I domain	2h7gX01
3.90.15.10	Alpha Beta	Alpha-Beta Complex	Topoisomerase I; Chain A, domain 3	Topoisomerase I; Chain A, domain 3	2h7gX02

2F4QA 1K4SA 2B9SA 1SEUA 1TL8A 1SC7A 1RRJA 1A35A 2H7GX 1K4TA 1VCCA 1LPQA 1A36A 3IGCA 1A31A 1R49A 1T8IA 3M4AA 1EJ9A 1A41A 1RR8C 2H7FX 1NH3A
chains in the Genus database with same CATH superfamily

2F4QA 1K4SA 2B9SA 1SEUA 1TL8A 1SC7A 1RRJA 1A35A 2H7GX 1K4TA 1VCCA 1LPQA 1A36A 3IGCA 1A31A 1R49A 1T8IA 3M4AA 1EJ9A 1A41A 1RR8C 2H7FX 1NH3A
chains in the Genus database with same CATH topology

2F4QA 1K4SA 2B9SA 1SEUA 1TL8A 1SC7A 1RRJA 1A35A 2H7GX 1K4TA 1VCCA 1LPQA 1A36A 3IGCA 1A31A 1R49A 1T8IA 3M4AA 1EJ9A 1A41A 1RR8C 2H7FX 1NH3A
chains in the Genus database with same CATH homology

#chains in the Genus database with same CATH superfamily
 2F4Q A;  1K4S A;  2B9S A;  1SEU A;  1TL8 A;  1SC7 A;  1RRJ A;  1A35 A;  2H7G X;  1K4T A;  1VCC A;  1LPQ A;  1A36 A;  3IGC A;  1A31 A;  1R49 A;  1T8I A;  3M4A A;  1EJ9 A;  1A41 A;  1RR8 C;  2H7F X;  1NH3 A; 
#chains in the Genus database with same CATH topology
 2F4Q A;  1K4S A;  2B9S A;  1SEU A;  1TL8 A;  1SC7 A;  1RRJ A;  1A35 A;  2H7G X;  1K4T A;  1VCC A;  1LPQ A;  1A36 A;  3IGC A;  1A31 A;  1R49 A;  1T8I A;  3M4A A;  1EJ9 A;  1A41 A;  1RR8 C;  2H7F X;  1NH3 A; 
#chains in the Genus database with same CATH homology
 2F4Q A;  1K4S A;  2B9S A;  1SEU A;  1TL8 A;  1SC7 A;  1RRJ A;  1A35 A;  2H7G X;  1K4T A;  1VCC A;  1LPQ A;  1A36 A;  3IGC A;  1A31 A;  1R49 A;  1T8I A;  3M4A A;  1EJ9 A;  1A41 A;  1RR8 C;  2H7F X;  1NH3 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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2H7GX

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations