3VM1 | Genus

Total Genus 192

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	192
sequence length	538
structure length	538
Chain Sequence	VAAERLEPRVEEKDGYWILKEQFRKGINPQEKVKIEKEPMKLFMENGIEELAKIPIEEIDQSKLTKDDIDVRLKWLGLFHRRKNQYGRFMMRLKLPNGVTTSAQTRYLASVIRKYGKEGCADITTRQNWQIRGVVLPDVPEILKGLAEVGLTSLQSGMDNVRNPVGNPLAGIDPEEIVDTRPYTNLLSQFITGNSRGNPAVSNLPRKWKPCVVGSHDLYEHPHINDLAYMPATKDGRFGFNLLVGGFFSAKRCDEAIPLDAWVPADDVVPVCRAILEAFRDLGFRGNRQKCRMMWLIDELGVEGFRAEVEKRMPQQQLERASPEDLVQKQWERRDYLGVHPQKQEGYSFIGLHIPVGRVQADDMDELARLADEYGSGEIRLTVEQNIIIPNIETSKIEALLKEPVLSTFSPDPPILMKGLVACTGNQFCGQAIIETKARSLKITEEVQRQVSLTKPVRMHWTGCPNTCAQVQVADIGFMGCLTRDKNGKTVEGADVFLGGRIGSDSHLGEVYKKAVPCDDLVPLVVDLLVNNFGAVPR

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/5d0352f86b155ddeeec93be2/pdb.gz

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The Resolver thinks Pdb

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Time for openFile(/file/5d0352f86b155ddeeec93be2/pdb.gz): 1155 ms

reading 538 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

538 atoms created

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

Time for creating model: 41 ms

Adding embedded #jmolscript: select ({0:537});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	Oxidoreductase
source organism	Nicotiana tabacum
publication title	X-ray crystal structure of a mutant assimilatory nitrite reductase that shows sulfite reductase-like activity pubmed doi rcsb
molecule keywords	Nitrite reductase
total genus	192
structure length	538
sequence length	538
ec nomenclature	ec 1.7.7.1: Ferredoxin--nitrite reductase.
pdb deposition date	2011-12-05

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF01077	NIR_SIR	Nitrite and sulphite reductase 4Fe-4S domain
A	PF03460	NIR_SIR_ferr	Nitrite/Sulfite reductase ferredoxin-like half domain

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

cath code	Class	Architecture	Topology	Homology	Domain
3.30.413.10	Alpha Beta	2-Layer Sandwich	Sulfite Reductase Hemoprotein; domain 1	Sulfite Reductase Hemoprotein, domain 1	3vm1A02
3.30.413.10	Alpha Beta	2-Layer Sandwich	Sulfite Reductase Hemoprotein; domain 1	Sulfite Reductase Hemoprotein, domain 1	3vm1A03
3.90.480.20	Alpha Beta	Alpha-Beta Complex	Sulfite Reductase Hemoprotein; domain 2	Sulfite Reductase Hemoprotein; domain 2	3vm1A01

1ZJ9A 3VLZA 4G38A 3MM7B 3MM6B 3OR1B 4S3BA 2V4JB 3B0JA 3MMBB 4S3EA 3MM5A 4S3AA 3VLYA 4S23A 6GEPA 3MMCB 3MM7A 3MM6A 3VM1A 2XSJB 3B0LA 4G39A 4S39A 2V4JA 3MMBA 3OR1A 3VLXA 3VM0A 8GEPA 3GEOA 3MM8B 3MMCA 3OR2B 4S3DA 3VKQA 4AOPA 2XSJA 2GEPA 5AOPA 3B0MA 3B0NA 4S38A 3VKSA 3MM8A 3MM9A 3OR2A 2AKJA 4GEPA 3VKPA 3MMAB 5GEPA 3AOPA 1ZJ8A 4G9PA 3MM9B 4S3FA 3NOYA 1AOPA 4S3CA 3VKRA 3VKTA 2AOPA 3B0GA 3MMAA 4HTRA 3B0HA 7GEPA 2Y0FA 3MM5B
chains in the Genus database with same CATH superfamily

#chains in the Genus database with same CATH superfamily
 1ZJ9 A;  3VLZ A;  4G38 A;  3MM7 B;  3MM6 B;  3OR1 B;  4S3B A;  2V4J B;  3B0J A;  3MMB B;  4S3E A;  3MM5 A;  4S3A A;  3VLY A;  4S23 A;  6GEP A;  3MMC B;  3MM7 A;  3MM6 A;  3VM1 A;  2XSJ B;  3B0L A;  4G39 A;  4S39 A;  2V4J A;  3MMB A;  3OR1 A;  3VLX A;  3VM0 A;  8GEP A;  3GEO A;  3MM8 B;  3MMC A;  3OR2 B;  4S3D A;  3VKQ A;  4AOP A;  2XSJ A;  2GEP A;  5AOP A;  3B0M A;  3B0N A;  4S38 A;  3VKS A;  3MM8 A;  3MM9 A;  3OR2 A;  2AKJ A;  4GEP A;  3VKP A;  3MMA B;  5GEP A;  3AOP A;  1ZJ8 A;  4G9P A;  3MM9 B;  4S3F A;  3NOY A;  1AOP A;  4S3C A;  3VKR A;  3VKT A;  2AOP A;  3B0G A;  3MMA A;  4HTR A;  3B0H A;  7GEP A;  2Y0F A;  3MM5 B; 
#chains in the Genus database with same CATH topology
 1ZJ9 A;  3VLZ A;  4G38 A;  3MM7 B;  3MM6 B;  3OR1 B;  4S3B A;  2V4J B;  3B0J A;  3MMB B;  4S3E A;  3MM5 A;  4S3A A;  3VLY A;  4S23 A;  6GEP A;  3MMC B;  3MM7 A;  3MM6 A;  3VM1 A;  2XSJ B;  3B0L A;  4G39 A;  4S39 A;  2V4J A;  3MMB A;  3OR1 A;  3VLX A;  3VM0 A;  8GEP A;  3GEO A;  3MM8 B;  3MMC A;  3OR2 B;  4S3D A;  3VKQ A;  4AOP A;  2XSJ A;  2GEP A;  5AOP A;  3B0M A;  3B0N A;  4S38 A;  3VKS A;  3MM8 A;  3MM9 A;  3OR2 A;  2AKJ A;  4GEP A;  3VKP A;  3MMA B;  5GEP A;  3AOP A;  1ZJ8 A;  4G9P A;  3MM9 B;  4S3F A;  3NOY A;  1AOP A;  4S3C A;  3VKR A;  3VKT A;  2AOP A;  3B0G A;  3MMA A;  4HTR A;  3B0H A;  7GEP A;  2Y0F A;  3MM5 B; 
#chains in the Genus database with same CATH homology
 1ZJ9 A;  3VLZ A;  4G38 A;  3MM7 B;  3MM6 B;  3OR1 B;  4S3B A;  2V4J B;  3B0J A;  3MMB B;  4S3E A;  3MM5 A;  4S3A A;  3VLY A;  4S23 A;  6GEP A;  3MMC B;  3MM7 A;  3MM6 A;  3VM1 A;  2XSJ B;  3B0L A;  4G39 A;  4S39 A;  2V4J A;  3MMB A;  3OR1 A;  3VLX A;  3VM0 A;  8GEP A;  3GEO A;  3MM8 B;  3MMC A;  3OR2 B;  4S3D A;  3VKQ A;  4AOP A;  2XSJ A;  2GEP A;  5AOP A;  3B0M A;  3B0N A;  4S38 A;  3VKS A;  3MM8 A;  3MM9 A;  3OR2 A;  2AKJ A;  4GEP A;  3VKP A;  3MMA B;  5GEP A;  3AOP A;  1ZJ8 A;  4G9P A;  3MM9 B;  4S3F A;  3NOY A;  1AOP A;  4S3C A;  3VKR A;  3VKT A;  2AOP A;  3B0G A;  3MMA A;  4HTR A;  3B0H A;  7GEP A;  2Y0F A;  3MM5 B;

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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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3VM1A

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

pfam database annotations