1KMD | Genus

Total Genus 17

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	17
sequence length	117
structure length	117
Chain Sequence	KMSEKLRIKVDDVKINPKYVLYGVSTPNKRLYKRYSEFWKLKTRLERDVGSTIPYDFPEKPGVLDRRWQRRYDDPEMIDERRIGLERFLNELYNDRFDSRWRDTKIAQDFLQLSKPN

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/5d29acacc7644b0c19bd7d09/pdb.gz

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The Resolver thinks Pdb

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

Time for openFile(/file/5d29acacc7644b0c19bd7d09/pdb.gz): 2546 ms

reading 117 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

117 atoms created

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

Time for creating model: 19 ms

Adding embedded #jmolscript: select ({0:116});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	Endocytosis/exocytosis
source organism	Saccharomyces cerevisiae
publication title	Solution structure of the Vam7p PX domain. pubmed doi rcsb
molecule keywords	Vacuolar morphogenesis protein VAM7
total genus	17
structure length	117
sequence length	117
ec nomenclature
pdb deposition date	2001-12-14

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF00787	PX	PX domain

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

cath code	Class	Architecture	Topology	Homology	Domain
3.30.1520.10	Alpha Beta	2-Layer Sandwich	PX Domain	Phox-like domain	1kmdA00

1OCUA 4P2JA 2V14A 4AKVA 4AZ9A 4IKBA 4OXWA 2YPSA 3P0CA 4PQPA 3LUIA 1XTEA 2CSKA 4PQOA 1GD5A 3DYTA 3FOGA 2L73A 1KMDA 2AR5A 4ON3A 1KQ6A 1XTNA 2DYBA 4P2IA 2V6VA 4IKDA 2I4KA 2RAJA 3HPBA 4IKBB 4BGJA 2RAKA 3HPCX 4PZGA 3IQ2A 2ETTA 2CZOA 2RAIA 1H6HA 1O7KA 2WWEA 4HASA 2REAA 1OCSA 2IWLX 2REDA
chains in the Genus database with same CATH superfamily

#chains in the Genus database with same CATH superfamily
 1OCU A;  4P2J A;  2V14 A;  4AKV A;  4AZ9 A;  4IKB A;  4OXW A;  2YPS A;  3P0C A;  4PQP A;  3LUI A;  1XTE A;  2CSK A;  4PQO A;  1GD5 A;  3DYT A;  3FOG A;  2L73 A;  1KMD A;  2AR5 A;  4ON3 A;  1KQ6 A;  1XTN A;  2DYB A;  4P2I A;  2V6V A;  4IKD A;  2I4K A;  2RAJ A;  3HPB A;  4IKB B;  4BGJ A;  2RAK A;  3HPC X;  4PZG A;  3IQ2 A;  2ETT A;  2CZO A;  2RAI A;  1H6H A;  1O7K A;  2WWE A;  4HAS A;  2REA A;  1OCS A;  2IWL X;  2RED A; 
#chains in the Genus database with same CATH topology
 1OCU A;  4P2J A;  2V14 A;  4AKV A;  4AZ9 A;  4IKB A;  4OXW A;  2YPS A;  3P0C A;  4PQP A;  3LUI A;  1XTE A;  2CSK A;  4PQO A;  1GD5 A;  3DYT A;  3FOG A;  2L73 A;  1KMD A;  2AR5 A;  4ON3 A;  1KQ6 A;  1XTN A;  2DYB A;  4P2I A;  2V6V A;  4IKD A;  2I4K A;  2RAJ A;  3HPB A;  4IKB B;  4BGJ A;  2RAK A;  3HPC X;  4PZG A;  3IQ2 A;  2ETT A;  2CZO A;  2RAI A;  1H6H A;  1O7K A;  2WWE A;  4HAS A;  2REA A;  1OCS A;  2IWL X;  2RED A; 
#chains in the Genus database with same CATH homology
 1OCU A;  4P2J A;  2V14 A;  4AKV A;  4AZ9 A;  4IKB A;  4OXW A;  2YPS A;  3P0C A;  4PQP A;  3LUI A;  1XTE A;  2CSK A;  4PQO A;  1GD5 A;  3DYT A;  3FOG A;  2L73 A;  1KMD A;  2AR5 A;  4ON3 A;  1KQ6 A;  1XTN A;  2DYB A;  4P2I A;  2V6V A;  4IKD A;  2I4K A;  2RAJ A;  3HPB A;  4IKB B;  4BGJ A;  2RAK A;  3HPC X;  4PZG A;  3IQ2 A;  2ETT A;  2CZO A;  2RAI A;  1H6H A;  1O7K A;  2WWE A;  4HAS A;  2REA A;  1OCS A;  2IWL X;  2RED 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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1KMDA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations