2WDQ | Genus

Total Genus 48

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	48
sequence length	121
structure length	121
Chain Sequence	QRPVNLDLQTIRFPITAIASILHRVSGVITFVAVGILLWLLGTSLSSPEGFEQASAIMGSFFVKFIMWGILTALAYHVVVGIRHMMMDFGYLEETFEAGKRSAKISFVITVVLSLLAGVLV

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/5cfdc5f9c5f9da08f4d06d84/pdb.gz): 1713 ms

reading 121 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

121 atoms created

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

Time for creating model: 17 ms

Adding embedded #jmolscript: select ({0:120});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	48
structure length	121
sequence length	121
chains with identical sequence	G, K
ec nomenclature
pdb deposition date	2009-03-25

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
C	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	2wdqC00

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

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

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

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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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2WDQC

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations