1BDS | Genus

Total Genus 4

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	4
sequence length	43
structure length	43
Chain Sequence	AAPCFCSGKPGRGDLWILRGTCPGGYGYTSNCYKWPNICCYPH

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/5cfac74123a75cd80531d09f/pdb.gz): 1125 ms

reading 43 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

43 atoms created

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

Time for creating model: 13 ms

Adding embedded #jmolscript: select ({0:42});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	Anti-hypertensive, anti-viral protein
source organism	Anemonia sulcata
publication title	Determination of the three-dimensional solution structure of the antihypertensive and antiviral protein BDS-I from the sea anemone Anemonia sulcata: a study using nuclear magnetic resonance and hybrid distance geometry-dynamical simulated annealing. pubmed doi rcsb
molecule keywords	BDS-I
total genus	4
structure length	43
sequence length	43
ec nomenclature
pdb deposition date	1988-11-14

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF07936	Defensin_4	Potassium-channel blocking toxin

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	1bdsA00

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

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

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

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

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations