3SN2 | Genus

Total Genus 226

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	226
sequence length	888
structure length	848
Chain Sequence	SNPFAYLAEPLDPAQPGKKFFNLNKLDYSRYGRLPFSIRVLLEAAVRNCDKFLVKKEDIENILNWNVTQHMNIEVPFKPARVILQDFTGVPSVVDFAAMRDAVKKLGGDPEKINPICPVDLVIDFERNRERFEFLKWGSKAFRNMRIIPPGSGIIHQVNLEYLARVVFDQDGYYYPDSLVGTDSHTTMIDGLGVLGWGVGGIEAEAVMLGQPISMVLPQVIGYRLMGKPHPLVTSTDIVLTITKHLRQVGVVGKFVEFFGPGVAQLSIADRATIANMCPEYGATATFFPVDEVSIKYLVQTGRDESKVKQIRKYLQAVGMFRDYSDPSQDPDFTQVVELDLKTVVPCCSGPKRPQDKVAVSDMKKDFESCLGAKQGFKGFQVAPDHHNDHKTFIYNDSEFTLSHGSVVIAAITSSTNTSNPSVMLGAGLLAKKAVDAGLNVKPYVKTSLSPGSGVVTYYLRESGVMPYLSQLGFDVVPLPEPVVEAITQGDLVAVGVLSGNRNFEGRVHPNTRANYLASPPLVIAYAIAGTIRIDFEKEPLGTNAKGQQVFLRDIWPTREEIQAVERQYVIPGMFTEVYQKIETVNASSDKLYLWNPKSTYIKSPPFFENLTLDLQPPKSIVDAYVLLNLGDSVTTDHISPAGNIARNSPAARYLTNRGLTPREFNSYGSRRGNDAIMARGTFANIRLLNRFLNKQAPQTIHLPSGETLDVFDAAERYQQEGHPLIVLAGKEYGSGSSRDWAAKGPFLLGIKAVLAESYERIHRSNLVGMGVIPLEYLPGENADSLGLTGRERYTIIIPENLTPRMHVQVKLDTGKTFQAVIRFDTDVELTYFHNGGILNYMIRKMAK

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/5d266d478c948fa0009ecfcb/pdb.gz): 1576 ms

reading 848 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

848 atoms created

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

Time for creating model: 63 ms

Adding embedded #jmolscript: select ({0:847});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

molecule tags	Lyase/rna
source organism	Oryctolagus cuniculus
publication title	Accommodating variety in iron-responsive elements: Crystal structure of transferrin receptor 1 B IRE bound to iron regulatory protein 1. pubmed doi rcsb
molecule keywords	Cytoplasmic aconitate hydratase
total genus	226
structure length	848
sequence length	888
ec nomenclature	ec 4.2.1.3: Aconitate hydratase.
pdb deposition date	2011-06-28

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF00330	Aconitase	Aconitase family (aconitate hydratase)
A	PF00694	Aconitase_C	Aconitase C-terminal domain

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

cath code	Class	Architecture	Topology	Homology	Domain
3.20.19.10	Alpha Beta	Alpha-Beta Barrel	Aconitase; domain 4	Aconitase, domain 4	3sn2A03
3.30.499.10	Alpha Beta	2-Layer Sandwich	Aconitase; domain 3	Aconitase, domain 3	3sn2A02
3.30.499.20	Alpha Beta	2-Layer Sandwich	Aconitase; domain 3	Aconitase; domain 3	3sn2A01

4KP1A 1C97A 4NQYA 2HCUA 1L5JA 1AMIA 3H5EA 2B3YA 1FGHA 3H5JA 1AMJA 1B0MA 5ACNA 1NITA 1V7LA 1NISA 2B3XA 3H5HA 1B0KA 6ACNA 3SN2A 3Q3WA 7ACNA 1B0JA 1C96A 2PKPA 3VBAA 8ACNA 4KP2A 3SNPA 1ACOA
chains in the Genus database with same CATH superfamily

#chains in the Genus database with same CATH superfamily
 4KP1 A;  1C97 A;  4NQY A;  2HCU A;  1L5J A;  1AMI A;  3H5E A;  2B3Y A;  1FGH A;  3H5J A;  1AMJ A;  1B0M A;  5ACN A;  1NIT A;  1V7L A;  1NIS A;  2B3X A;  3H5H A;  1B0K A;  6ACN A;  3SN2 A;  3Q3W A;  7ACN A;  1B0J A;  1C96 A;  2PKP A;  3VBA A;  8ACN A;  4KP2 A;  3SNP A;  1ACO A; 
#chains in the Genus database with same CATH topology
 4KP1 A;  1C97 A;  4NQY A;  2HCU A;  1L5J A;  1AMI A;  3H5E A;  2B3Y A;  1FGH A;  3H5J A;  1AMJ A;  1B0M A;  5ACN A;  1NIT A;  1V7L A;  1NIS A;  2B3X A;  3H5H A;  1B0K A;  6ACN A;  3SN2 A;  3Q3W A;  7ACN A;  1B0J A;  1C96 A;  2PKP A;  3VBA A;  8ACN A;  4KP2 A;  3SNP A;  1ACO A; 
#chains in the Genus database with same CATH homology
 4KP1 A;  1C97 A;  4NQY A;  2HCU A;  1L5J A;  1AMI A;  3H5E A;  2B3Y A;  1FGH A;  3H5J A;  1AMJ A;  1B0M A;  5ACN A;  1NIT A;  1V7L A;  1NIS A;  2B3X A;  3H5H A;  1B0K A;  6ACN A;  3SN2 A;  3Q3W A;  7ACN A;  1B0J A;  1C96 A;  2PKP A;  3VBA A;  8ACN A;  4KP2 A;  3SNP A;  1ACO 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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3SN2A

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

pfam database annotations