4GV5 | Genus

Total Genus 10

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	10
sequence length	42
structure length	42
Chain Sequence	YKQCHKKGGHCFPKEKICLPPSSDFGKMDCRWRWKCCKKGSG

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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The Resolver thinks Pdb

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Time for openFile(/file/5d0030cd80cc945713e3fb1a/pdb.gz): 1191 ms

reading 42 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

42 atoms created

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

Time for creating model: 14 ms

Adding embedded #jmolscript: select ({0:41});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	Toxin
publication title	Structure of the polypeptide crotamine from the Brazilian rattlesnake Crotalus durissus terrificus. pubmed doi rcsb
molecule keywords	Crotamine Ile-19
total genus	10
structure length	42
sequence length	42
chains with identical sequence	B, C
ec nomenclature
pdb deposition date	2012-08-30

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

cath code	Class	Architecture	Topology	Homology	Domain
2.20.20.10	Mainly Beta	Single Sheet	Anthopleurin-A	Anthopleurin-A	4gv5A00

2SH1A 2H9XA 1Z99A 1ZUFA 1B8WA 1ATXA 4GV5A 1WQKA 1H5OA 2MN3A 1APFA 1BDSA 2JTOA 1WXNA 1D6BA 1SHIA 1SH1A 3D4UB 3LMSB 2K2XA 2BDSA 2RNGA 1ZLIB 1AHLA 1ZUEA 1ZLHB 2MUBA
chains in the Genus database with same CATH superfamily

2IKDA 2SH1A 1EL6A 2H9XA 1Z99A 1ZUFA 1B8WA 2QSHA 1GKUB 1ATXA 2DLAA 4GV5A 2HJEA 2HJ9C 3C30A 3KEZA 2IKEA 1WQKA 1H5OA 2MN3A 1APFA 3MCXA 1BDSA 2JTOA 1WXNA 1D6BA 1SHIA 1ZHHB 1SH1A 3D4UB 3LMSB 2QSGA 3IF4A 2BDSA 2K2XA 1ZLIB 2RNGA 2XXLA 4YIRA 1ZUEA 1AHLA 3MYVA 1ZLHB 1GL9B 2B9KA 2QSFA 3C38A 2JR3A 2MUBA
chains in the Genus database with same CATH topology

2IKDA 2SH1A 2H9XA 1Z99A 1ZUFA 1B8WA 2QSHA 1ATXA 2DLAA 4GV5A 2HJEA 2HJ9C 3C30A 3KEZA 2IKEA 1WQKA 1H5OA 2MN3A 1APFA 3MCXA 1BDSA 2JTOA 1WXNA 1D6BA 1SHIA 1ZHHB 1SH1A 3D4UB 3LMSB 2QSGA 2BDSA 2K2XA 1ZLIB 2RNGA 2XXLA 4YIRA 1ZUEA 1AHLA 3MYVA 1ZLHB 2B9KA 2QSFA 3C38A 2JR3A 2MUBA
chains in the Genus database with same CATH homology

#chains in the Genus database with same CATH superfamily
 2SH1 A;  2H9X A;  1Z99 A;  1ZUF A;  1B8W A;  1ATX A;  4GV5 A;  1WQK A;  1H5O A;  2MN3 A;  1APF A;  1BDS A;  2JTO A;  1WXN A;  1D6B A;  1SHI A;  1SH1 A;  3D4U B;  3LMS B;  2K2X A;  2BDS A;  2RNG A;  1ZLI B;  1AHL A;  1ZUE A;  1ZLH B;  2MUB A; 
#chains in the Genus database with same CATH topology
 2IKD A;  2SH1 A;  1EL6 A;  2H9X A;  1Z99 A;  1ZUF A;  1B8W A;  2QSH A;  1GKU B;  1ATX A;  2DLA A;  4GV5 A;  2HJE A;  2HJ9 C;  3C30 A;  3KEZ A;  2IKE A;  1WQK A;  1H5O A;  2MN3 A;  1APF A;  3MCX A;  1BDS A;  2JTO A;  1WXN A;  1D6B A;  1SHI A;  1ZHH B;  1SH1 A;  3D4U B;  3LMS B;  2QSG A;  3IF4 A;  2BDS A;  2K2X A;  1ZLI B;  2RNG A;  2XXL A;  4YIR A;  1ZUE A;  1AHL A;  3MYV A;  1ZLH B;  1GL9 B;  2B9K A;  2QSF A;  3C38 A;  2JR3 A;  2MUB A; 
#chains in the Genus database with same CATH homology
 2IKD A;  2SH1 A;  2H9X A;  1Z99 A;  1ZUF A;  1B8W A;  2QSH A;  1ATX A;  2DLA A;  4GV5 A;  2HJE A;  2HJ9 C;  3C30 A;  3KEZ A;  2IKE A;  1WQK A;  1H5O A;  2MN3 A;  1APF A;  3MCX A;  1BDS A;  2JTO A;  1WXN A;  1D6B A;  1SHI A;  1ZHH B;  1SH1 A;  3D4U B;  3LMS B;  2QSG A;  2BDS A;  2K2X A;  1ZLI B;  2RNG A;  2XXL A;  4YIR A;  1ZUE A;  1AHL A;  3MYV A;  1ZLH B;  2B9K A;  2QSF A;  3C38 A;  2JR3 A;  2MUB 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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4GV5A

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN