5F3M | Genus

Total Genus 32

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	32
sequence length	120
structure length	120
Chain Sequence	MDKIYIHDMEFYGYHGVFPEENKLGQRFKVDLTVELDLKRAGESDDLEHSVNYGELFELCRKVVEDRTYKLVESIAENIATDILKQYESISRCTIKVIKPDPPIPGHYRAVAVEITRERP

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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reading 120 atoms

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1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.

Default Van der Waals type for model set to Jmol

120 atoms created

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

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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

publication title	Crystal structure of dihydroneopterin aldolase from Bacillus anthracis complexed with L-neopterin at 1.5 Angstroms resolution . rcsb
molecule keywords	7,8-dihydroneopterin aldolase
molecule tags	Isomerase
source organism	Bacillus anthracis str. 'ames ancestor'
total genus	32
structure length	120
sequence length	120
chains with identical sequence	B
ec nomenclature	ec 4.1.2.25: Dihydroneopterin aldolase.
pdb deposition date	2015-12-03

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF02152	FolB	Dihydroneopterin aldolase

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	5f3mA00

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

#chains in the Genus database with same CATH superfamily
 5FAR A;  1NBU B;  1RS4 A;  2NM2 A;  1FBX A;  1WUQ A;  2CG8 A;  2NM3 A;  4F8B A;  1DHN A;  1WPL A;  5F3M A;  3RZP A;  1IS7 A;  1WM9 A;  1RSI A;  3O1K A;  1RSD A;  4UQF A;  3RJ4 A;  1GTP A;  1NBU C;  1RRY A;  1U68 A;  3BP1 A;  3UXJ A;  3UXV A;  1SQL A;  2O90 A;  3R2E A;  1RRI A;  1FB1 A;  1N3S A;  1A8R A;  1N3T A;  1WUR A;  4GHM A;  1RS2 A;  1RRW A;  1N3R A;  1B9L A;  1Z9W A;  4IQI A;  1NBU A;  1IS8 A;  1A9C A;  4AEY A;  4FGC A;  3S19 A;  2DHN A;  3V9O A;  4DU6 A; 
#chains in the Genus database with same CATH topology
 5FAR A;  1NBU B;  1RS4 A;  2NM2 A;  1FBX A;  1WUQ A;  2CG8 A;  2NM3 A;  4F8B A;  1DHN A;  1WPL A;  5F3M A;  3RZP A;  1IS7 A;  1WM9 A;  1RSI A;  3O1K A;  1RSD A;  4UQF A;  3RJ4 A;  1GTP A;  1NBU C;  1RRY A;  1U68 A;  3BP1 A;  3UXJ A;  3UXV A;  1SQL A;  2O90 A;  3R2E A;  1RRI A;  1FB1 A;  1N3S A;  1A8R A;  1N3T A;  1WUR A;  4GHM A;  1RS2 A;  1RRW A;  1N3R A;  1B9L A;  1Z9W A;  4IQI A;  1NBU A;  1IS8 A;  1A9C A;  4AEY A;  4FGC A;  3S19 A;  2DHN A;  3V9O A;  4DU6 A; 
#chains in the Genus database with same CATH homology
 5FAR A;  1NBU B;  1RS4 A;  2NM2 A;  1FBX A;  1WUQ A;  2CG8 A;  2NM3 A;  4F8B A;  1DHN A;  1WPL A;  5F3M A;  3RZP A;  1IS7 A;  1WM9 A;  1RSI A;  3O1K A;  1RSD A;  4UQF A;  3RJ4 A;  1GTP A;  1NBU C;  1RRY A;  1U68 A;  3BP1 A;  3UXJ A;  3UXV A;  1SQL A;  2O90 A;  3R2E A;  1RRI A;  1FB1 A;  1N3S A;  1A8R A;  1N3T A;  1WUR A;  4GHM A;  1RS2 A;  1RRW A;  1N3R A;  1B9L A;  1Z9W A;  4IQI A;  1NBU A;  1IS8 A;  1A9C A;  4AEY A;  4FGC A;  3S19 A;  2DHN A;  3V9O A;  4DU6 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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5F3MA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations