4F8B | Genus

Total Genus 41

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	41
sequence length	139
structure length	139
Chain Sequence	NYLFEYAPDVLESFPNKHVNRDYFVKFNCPEFTSLCPKTGQPDFATIYISYIPDEKMVESKSLKLYLFSFRNHGDFHEDCMNIIMNDLIELMDPRYIEVWGKFTPRGGISIDPYTNYGKPGTKYEKMAEYRMMNHDLYP

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

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

Time for openFile(/file/5d03c1d2fda24889999822ef/pdb.gz): 2280 ms

reading 139 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

139 atoms created

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

Time for creating model: 23 ms

Adding embedded #jmolscript: select ({0:138});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	Oxidoreductase
source organism	Bacillus subtilis subsp. subtilis
publication title	Structural basis of biological nitrile reduction. pubmed doi rcsb
molecule keywords	NADPH-dependent 7-cyano-7-deazaguanine reductase
total genus	41
structure length	139
sequence length	139
chains with identical sequence	B, C, D, E
ec nomenclature	ec 1.7.1.13: PreQ(1) synthase.
pdb deposition date	2012-05-17

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF14489	QueF	QueF-like protein

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

cath code	Class	Architecture	Topology	Homology	Domain
3.30.1130.10	Alpha Beta	2-Layer Sandwich	GTP Cyclohydrolase I, domain 2	GTP Cyclohydrolase I, domain 2	4f8bA00

2DHNA 4GHMA 1WPLA 3UXJA 4AEYA 1RSDA 1RRIA 3RJ4A 4DU6A 4IQIA 1IS7A 1RRWA 1WUQA 1N3RA 2CG8A 1U68A 1N3SA 4FGCA 1DHNA 1WURA 1N3TA 3BP1A 4F8BA 1FB1A 3O1KA 3RZPA 3S19A 1NBUA 1A9CA 1RRYA 3R2EA 5F3MA 2O90A 1A8RA 1SQLA 1Z9WA 1GTPA 1IS8A 2NM2A 4UQFA 5FARA 1B9LA 3UXVA 1RS2A 1NBUB 1RS4A 3V9OA 1RSIA 2NM3A 1NBUC 1WM9A 1FBXA
chains in the Genus database with same CATH superfamily

#chains in the Genus database with same CATH superfamily
 2DHN A;  4GHM A;  1WPL A;  3UXJ A;  4AEY A;  1RSD A;  1RRI A;  3RJ4 A;  4DU6 A;  4IQI A;  1IS7 A;  1RRW A;  1WUQ A;  1N3R A;  2CG8 A;  1U68 A;  1N3S A;  4FGC A;  1DHN A;  1WUR A;  1N3T A;  3BP1 A;  4F8B A;  1FB1 A;  3O1K A;  3RZP A;  3S19 A;  1NBU A;  1A9C A;  1RRY A;  3R2E A;  5F3M A;  2O90 A;  1A8R A;  1SQL A;  1Z9W A;  1GTP A;  1IS8 A;  2NM2 A;  4UQF A;  5FAR A;  1B9L A;  3UXV A;  1RS2 A;  1NBU B;  1RS4 A;  3V9O A;  1RSI A;  2NM3 A;  1NBU C;  1WM9 A;  1FBX A; 
#chains in the Genus database with same CATH topology
 2DHN A;  4GHM A;  1WPL A;  3UXJ A;  4AEY A;  1RSD A;  1RRI A;  3RJ4 A;  4DU6 A;  4IQI A;  1IS7 A;  1RRW A;  1WUQ A;  1N3R A;  2CG8 A;  1U68 A;  1N3S A;  4FGC A;  1DHN A;  1WUR A;  1N3T A;  3BP1 A;  4F8B A;  1FB1 A;  3O1K A;  3RZP A;  3S19 A;  1NBU A;  1A9C A;  1RRY A;  3R2E A;  5F3M A;  2O90 A;  1A8R A;  1SQL A;  1Z9W A;  1GTP A;  1IS8 A;  2NM2 A;  4UQF A;  5FAR A;  1B9L A;  3UXV A;  1RS2 A;  1NBU B;  1RS4 A;  3V9O A;  1RSI A;  2NM3 A;  1NBU C;  1WM9 A;  1FBX A; 
#chains in the Genus database with same CATH homology
 2DHN A;  4GHM A;  1WPL A;  3UXJ A;  4AEY A;  1RSD A;  1RRI A;  3RJ4 A;  4DU6 A;  4IQI A;  1IS7 A;  1RRW A;  1WUQ A;  1N3R A;  2CG8 A;  1U68 A;  1N3S A;  4FGC A;  1DHN A;  1WUR A;  1N3T A;  3BP1 A;  4F8B A;  1FB1 A;  3O1K A;  3RZP A;  3S19 A;  1NBU A;  1A9C A;  1RRY A;  3R2E A;  5F3M A;  2O90 A;  1A8R A;  1SQL A;  1Z9W A;  1GTP A;  1IS8 A;  2NM2 A;  4UQF A;  5FAR A;  1B9L A;  3UXV A;  1RS2 A;  1NBU B;  1RS4 A;  3V9O A;  1RSI A;  2NM3 A;  1NBU C;  1WM9 A;  1FBX 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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4F8BA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations