2AGM | Genus

Total Genus 22

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	22
sequence length	167
structure length	167
Chain Sequence	GSDGEPLVGGDTDDQLQGGSGADRLDGGAGDDILDGGAGRDRLSGGAGADTFVFSAREDSYRTDTAVFNDLILDFEASEDRIDLSALGFSGLGDGYGGTLLLKTNAEGTRTYLKSFEADAEGRRFEVALDGDHTGDLSAANVVFAATGTTTELEVLGDSGTQAGAIV

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/5cfc9bdf67b23050319d8691/pdb.gz): 1786 ms

reading 167 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

167 atoms created

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

Time for creating model: 22 ms

Adding embedded #jmolscript: select ({0:166});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	Isomerase
source organism	Azotobacter vinelandii
publication title	NMR structure of the R-module: a parallel beta-roll subunit from an Azotobacter vinelandii mannuronan C-5 epimerase. pubmed doi rcsb
molecule keywords	Poly(beta-D-mannuronate) C5 epimerase 4
total genus	22
structure length	167
sequence length	167
ec nomenclature	ec 5.1.3.37: Mannuronan 5-epimerase.
pdb deposition date	2005-07-27

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF00353	HemolysinCabind	RTX calcium-binding nonapeptide repeat (4 copies)

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

cath code	Class	Architecture	Topology	Homology	Domain
2.150.10.10	Mainly Beta	2 Solenoid	Alkaline Protease, subunit P, domain 1	Serralysin-like metalloprotease, C-terminal	2agmA01

3U1RA 5D7WA 1H71P 1OM6A 3LAAA 1K7GA 3ULTA 5CVWA 1OM7A 1P9HA 2ZJ7A 3HDAP 1KAPP 1OM8A 1OMJA 3A70A 3A6ZA 1G9KA 2XQHA 3NTNA 1SMPA 3HBVP 5CXLA 1SATA 1AF0A 2QUAA 3VI1A 1AKLA 2AGMA 1SRPA 1JIWP 1K7QA 3LA9A 1GO7P 1GO8P 3S6LA 2YO1A 2QUBA 3HBUP 1O0QA 3HB2P 2YO0A 2Z8XA 2ML2A 2ZVDA 3WP8A 2Z8ZA 4I35A 1K7IA 2ZJ6A 1O0TA
chains in the Genus database with same CATH superfamily

3U1RA 5D7WA 1H71P 1OM6A 3LAAA 1K7GA 3ULTA 5CVWA 1OM7A 1P9HA 2ZJ7A 3HDAP 1KAPP 1OM8A 1OMJA 3A70A 3A6ZA 1G9KA 2XQHA 3NTNA 1SMPA 3HBVP 5CXLA 1SATA 1AF0A 2QUAA 3VI1A 1AKLA 2AGMA 4DT5A 1SRPA 1JIWP 1K7QA 3LA9A 1GO7P 1GO8P 3S6LA 2YO1A 2QUBA 3HBUP 1O0QA 3HB2P 2YO0A 2Z8XA 2ML2A 2ZVDA 3WP8A 2Z8ZA 4I35A 1K7IA 2ZJ6A 1O0TA
chains in the Genus database with same CATH topology

#chains in the Genus database with same CATH superfamily
 3U1R A;  5D7W A;  1H71 P;  1OM6 A;  3LAA A;  1K7G A;  3ULT A;  5CVW A;  1OM7 A;  1P9H A;  2ZJ7 A;  3HDA P;  1KAP P;  1OM8 A;  1OMJ A;  3A70 A;  3A6Z A;  1G9K A;  2XQH A;  3NTN A;  1SMP A;  3HBV P;  5CXL A;  1SAT A;  1AF0 A;  2QUA A;  3VI1 A;  1AKL A;  2AGM A;  1SRP A;  1JIW P;  1K7Q A;  3LA9 A;  1GO7 P;  1GO8 P;  3S6L A;  2YO1 A;  2QUB A;  3HBU P;  1O0Q A;  3HB2 P;  2YO0 A;  2Z8X A;  2ML2 A;  2ZVD A;  3WP8 A;  2Z8Z A;  4I35 A;  1K7I A;  2ZJ6 A;  1O0T A; 
#chains in the Genus database with same CATH topology
 3U1R A;  5D7W A;  1H71 P;  1OM6 A;  3LAA A;  1K7G A;  3ULT A;  5CVW A;  1OM7 A;  1P9H A;  2ZJ7 A;  3HDA P;  1KAP P;  1OM8 A;  1OMJ A;  3A70 A;  3A6Z A;  1G9K A;  2XQH A;  3NTN A;  1SMP A;  3HBV P;  5CXL A;  1SAT A;  1AF0 A;  2QUA A;  3VI1 A;  1AKL A;  2AGM A;  4DT5 A;  1SRP A;  1JIW P;  1K7Q A;  3LA9 A;  1GO7 P;  1GO8 P;  3S6L A;  2YO1 A;  2QUB A;  3HBU P;  1O0Q A;  3HB2 P;  2YO0 A;  2Z8X A;  2ML2 A;  2ZVD A;  3WP8 A;  2Z8Z A;  4I35 A;  1K7I A;  2ZJ6 A;  1O0T A; 
#chains in the Genus database with same CATH homology
 3U1R A;  5D7W A;  1H71 P;  1OM6 A;  3LAA A;  1K7G A;  3ULT A;  5CVW A;  1OM7 A;  1P9H A;  2ZJ7 A;  3HDA P;  1KAP P;  1OM8 A;  1OMJ A;  3A70 A;  3A6Z A;  1G9K A;  2XQH A;  3NTN A;  1SMP A;  3HBV P;  5CXL A;  1SAT A;  1AF0 A;  2QUA A;  3VI1 A;  1AKL A;  2AGM A;  1SRP A;  1JIW P;  1K7Q A;  3LA9 A;  1GO7 P;  1GO8 P;  3S6L A;  2YO1 A;  2QUB A;  3HBU P;  1O0Q A;  3HB2 P;  2YO0 A;  2Z8X A;  2ML2 A;  2ZVD A;  3WP8 A;  2Z8Z A;  4I35 A;  1K7I A;  2ZJ6 A;  1O0T 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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2AGMA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations