2WDR | Genus

Total Genus 44

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	44
sequence length	105
structure length	105
Chain Sequence	NGVHDFILVRATAIVLTLYIIYMVGFFATSGELTYEVWIGFFASAFTKVFTLLALFSILIHAWIGMWQVLTDYVKPLALRLMLQLVIVVALVVYVIYGFVVVWGV

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/5cfdc79820b281166df2154d/pdb.gz

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The Resolver thinks Pdb

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Time for openFile(/file/5cfdc79820b281166df2154d/pdb.gz): 3430 ms

reading 105 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

105 atoms created

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

Time for creating model: 18 ms

Adding embedded #jmolscript: select ({0:104});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	Escherichia coli
publication title	Structure of Escherichia Coli Succinate:Quinone Oxidoreductase with an Occupied and Empty Quinone- Binding Site. pubmed doi rcsb
molecule keywords	SUCCINATE DEHYDROGENASE FLAVOPROTEIN SUBUNIT
total genus	44
structure length	105
sequence length	105
chains with identical sequence	H, L
ec nomenclature
pdb deposition date	2009-03-25

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
D	PF01127	Sdh_cyt	Succinate dehydrogenase/Fumarate reductase transmembrane subunit

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

cath code	Class	Architecture	Topology	Homology	Domain
1.20.1300.10	Mainly Alpha	Up-down Bundle	3 helical TM bundles of succinate and fumarate reductases	Fumarate reductase/succinate dehydrogenase, transmembrane subunit	2wdrD00

2WDQC 3AEDC 3AE9C 4YSXC 4YTMC 1KF6D 1L0VC 1ZOYD 2WDRC 4YSZD 1NEKC 2WDVC 2H88D 2B76D 3CIRC 3VRAC 3P4SC 4YTNC 3AE8D 1NEND 3AEEC 3P4RD 3AE1D 3VR8D 2WQYD 2WU5C 3AE2D 3AE5C 2WU2C 3ABVC 3AE3D 3AE4D 2ACZC 2FBWD 3AEGC 3SFED 3AEFC 3AEBC 1ZP0C 1KFYC 4KX6C 5C3JD 1NEKD 1YQ3D 3AEAD 3P4PD 3VR9D 2WS3C 3SFDC 3AE7D 2H89C 3AE6C 3VRBC 5C2TC 3P4QC 4YXDC 4YTPC 4YSYD 3AECD 2WP9D 2WDQD 4YT0D 3AEDD 3AE9D 1QLBC 4YTMD 4YSXD 1L0VD 1YQ4C 1ZP0D 2WDRD 2WS3D 4YSZC 3SFDD 2BS4C 2WDVD 3CIRD 2H88C 3VRAD 3P4SD 4YTND 3VRBD 3AEED 3AE8C 1NENC 3P4QD 3P4RC 2WU5D 3VR8C 2WQYC 3AE5D 2WU2D 3ABVD 3AE3C 3AE4C 2ACZD 2BS3C 3AEGD 2FBWC 2BS2C 3AEBD 3AEFD 3SFEC 1YQ4D 2WP9C 1KF6C 1KFYD 4KX6D 1ZOYC 5C3JC 1YQ3C 3AEAC 1E7PC 3P4PC 3VR9C 4YSYC 2B76C 2H89D 3AE7C 3AE6D 5C2TD 4YXDD 3AE1C 4YTPD 3AE2C 4YT0C 3AECC
chains in the Genus database with same CATH superfamily

2WDQC 3AEDC 3AE9C 4YSXC 4YTMC 1KF6D 1L0VC 1ZOYD 2WDRC 4YSZD 4DDIA 1NEKC 2WDVC 2H88D 2B76D 3CIRC 3VRAC 3P4SC 4YTNC 3AE8D 1NEND 3AEEC 3P4RD 3AE1D 3VR8D 2WQYD 2WU5C 3AE2D 3AE5C 2WU2C 3ABVC 3VONA 3AE3D 3AE4D 2ACZC 2FBWD 3AEGC 4DDGA 3SFED 3AEFC 3AEBC 1ZP0C 1KFYC 4KX6C 5C3JD 1NEKD 1YQ3D 3AEAD 3P4PD 3VR9D 2WS3C 3SFDC 3AE7D 2H89C 4DHJA 3AE6C 3VRBC 5C2TC 3P4QC 4YXDC 4YTPC 4YSYD 3AECD 2WP9D 2WDQD 4YT0D 4DHZA 3AEDD 3AE9D 1QLBC 4YTMD 4YSXD 1L0VD 1YQ4C 1ZP0D 2WDRD 2WS3D 4YSZC 3SFDD 2BS4C 2WDVD 3CIRD 2H88C 3VRAD 4DHIB 3P4SD 4YTND 3VRBD 3AEED 3AE8C 1NENC 3P4QD 3P4RC 2WU5D 3VR8C 2WQYC 3AE5D 1TFFA 2WU2D 2ZFYA 3ABVD 3AE3C 3AE4C 2ACZD 2BS3C 4FJVA 3AEGD 4I6LA 2FBWC 2BS2C 3AEBD 3AEFD 3SFEC 1YQ4D 2WP9C 1KF6C 1KFYD 4KX6D 1ZOYC 5C3JC 4LDTA 1YQ3C 3AEAC 1E7PC 3P4PC 3VR9C 4YSYC 2B76C 2H89D 3AE7C 3AE6D 5C2TD 4YXDD 3AE1C 4YTPD 3AE2C 4YT0C 3AECC
chains in the Genus database with same CATH topology

#chains in the Genus database with same CATH superfamily
 2WDQ C;  3AED C;  3AE9 C;  4YSX C;  4YTM C;  1KF6 D;  1L0V C;  1ZOY D;  2WDR C;  4YSZ D;  1NEK C;  2WDV C;  2H88 D;  2B76 D;  3CIR C;  3VRA C;  3P4S C;  4YTN C;  3AE8 D;  1NEN D;  3AEE C;  3P4R D;  3AE1 D;  3VR8 D;  2WQY D;  2WU5 C;  3AE2 D;  3AE5 C;  2WU2 C;  3ABV C;  3AE3 D;  3AE4 D;  2ACZ C;  2FBW D;  3AEG C;  3SFE D;  3AEF C;  3AEB C;  1ZP0 C;  1KFY C;  4KX6 C;  5C3J D;  1NEK D;  1YQ3 D;  3AEA D;  3P4P D;  3VR9 D;  2WS3 C;  3SFD C;  3AE7 D;  2H89 C;  3AE6 C;  3VRB C;  5C2T C;  3P4Q C;  4YXD C;  4YTP C;  4YSY D;  3AEC D;  2WP9 D;  2WDQ D;  4YT0 D;  3AED D;  3AE9 D;  1QLB C;  4YTM D;  4YSX D;  1L0V D;  1YQ4 C;  1ZP0 D;  2WDR D;  2WS3 D;  4YSZ C;  3SFD D;  2BS4 C;  2WDV D;  3CIR D;  2H88 C;  3VRA D;  3P4S D;  4YTN D;  3VRB D;  3AEE D;  3AE8 C;  1NEN C;  3P4Q D;  3P4R C;  2WU5 D;  3VR8 C;  2WQY C;  3AE5 D;  2WU2 D;  3ABV D;  3AE3 C;  3AE4 C;  2ACZ D;  2BS3 C;  3AEG D;  2FBW C;  2BS2 C;  3AEB D;  3AEF D;  3SFE C;  1YQ4 D;  2WP9 C;  1KF6 C;  1KFY D;  4KX6 D;  1ZOY C;  5C3J C;  1YQ3 C;  3AEA C;  1E7P C;  3P4P C;  3VR9 C;  4YSY C;  2B76 C;  2H89 D;  3AE7 C;  3AE6 D;  5C2T D;  4YXD D;  3AE1 C;  4YTP D;  3AE2 C;  4YT0 C;  3AEC C; 
#chains in the Genus database with same CATH topology
 2WDQ C;  3AED C;  3AE9 C;  4YSX C;  4YTM C;  1KF6 D;  1L0V C;  1ZOY D;  2WDR C;  4YSZ D;  4DDI A;  1NEK C;  2WDV C;  2H88 D;  2B76 D;  3CIR C;  3VRA C;  3P4S C;  4YTN C;  3AE8 D;  1NEN D;  3AEE C;  3P4R D;  3AE1 D;  3VR8 D;  2WQY D;  2WU5 C;  3AE2 D;  3AE5 C;  2WU2 C;  3ABV C;  3VON A;  3AE3 D;  3AE4 D;  2ACZ C;  2FBW D;  3AEG C;  4DDG A;  3SFE D;  3AEF C;  3AEB C;  1ZP0 C;  1KFY C;  4KX6 C;  5C3J D;  1NEK D;  1YQ3 D;  3AEA D;  3P4P D;  3VR9 D;  2WS3 C;  3SFD C;  3AE7 D;  2H89 C;  4DHJ A;  3AE6 C;  3VRB C;  5C2T C;  3P4Q C;  4YXD C;  4YTP C;  4YSY D;  3AEC D;  2WP9 D;  2WDQ D;  4YT0 D;  4DHZ A;  3AED D;  3AE9 D;  1QLB C;  4YTM D;  4YSX D;  1L0V D;  1YQ4 C;  1ZP0 D;  2WDR D;  2WS3 D;  4YSZ C;  3SFD D;  2BS4 C;  2WDV D;  3CIR D;  2H88 C;  3VRA D;  4DHI B;  3P4S D;  4YTN D;  3VRB D;  3AEE D;  3AE8 C;  1NEN C;  3P4Q D;  3P4R C;  2WU5 D;  3VR8 C;  2WQY C;  3AE5 D;  1TFF A;  2WU2 D;  2ZFY A;  3ABV D;  3AE3 C;  3AE4 C;  2ACZ D;  2BS3 C;  4FJV A;  3AEG D;  4I6L A;  2FBW C;  2BS2 C;  3AEB D;  3AEF D;  3SFE C;  1YQ4 D;  2WP9 C;  1KF6 C;  1KFY D;  4KX6 D;  1ZOY C;  5C3J C;  4LDT A;  1YQ3 C;  3AEA C;  1E7P C;  3P4P C;  3VR9 C;  4YSY C;  2B76 C;  2H89 D;  3AE7 C;  3AE6 D;  5C2T D;  4YXD D;  3AE1 C;  4YTP D;  3AE2 C;  4YT0 C;  3AEC C; 
#chains in the Genus database with same CATH homology
 2WDQ C;  3AED C;  3AE9 C;  4YSX C;  4YTM C;  1KF6 D;  1L0V C;  1ZOY D;  2WDR C;  4YSZ D;  1NEK C;  2WDV C;  2H88 D;  2B76 D;  3CIR C;  3VRA C;  3P4S C;  4YTN C;  3AE8 D;  1NEN D;  3AEE C;  3P4R D;  3AE1 D;  3VR8 D;  2WQY D;  2WU5 C;  3AE2 D;  3AE5 C;  2WU2 C;  3ABV C;  3AE3 D;  3AE4 D;  2ACZ C;  2FBW D;  3AEG C;  3SFE D;  3AEF C;  3AEB C;  1ZP0 C;  1KFY C;  4KX6 C;  5C3J D;  1NEK D;  1YQ3 D;  3AEA D;  3P4P D;  3VR9 D;  2WS3 C;  3SFD C;  3AE7 D;  2H89 C;  3AE6 C;  3VRB C;  5C2T C;  3P4Q C;  4YXD C;  4YTP C;  4YSY D;  3AEC D;  2WP9 D;  2WDQ D;  4YT0 D;  3AED D;  3AE9 D;  1QLB C;  4YTM D;  4YSX D;  1L0V D;  1YQ4 C;  1ZP0 D;  2WDR D;  2WS3 D;  4YSZ C;  3SFD D;  2BS4 C;  2WDV D;  3CIR D;  2H88 C;  3VRA D;  3P4S D;  4YTN D;  3VRB D;  3AEE D;  3AE8 C;  1NEN C;  3P4Q D;  3P4R C;  2WU5 D;  3VR8 C;  2WQY C;  3AE5 D;  2WU2 D;  3ABV D;  3AE3 C;  3AE4 C;  2ACZ D;  2BS3 C;  3AEG D;  2FBW C;  2BS2 C;  3AEB D;  3AEF D;  3SFE C;  1YQ4 D;  2WP9 C;  1KF6 C;  1KFY D;  4KX6 D;  1ZOY C;  5C3J C;  1YQ3 C;  3AEA C;  1E7P C;  3P4P C;  3VR9 C;  4YSY C;  2B76 C;  2H89 D;  3AE7 C;  3AE6 D;  5C2T D;  4YXD D;  3AE1 C;  4YTP D;  3AE2 C;  4YT0 C;  3AEC C;

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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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2WDRD

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations