2WDR | 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	122
structure length	122
Chain Sequence	QRPVNLDLQTIRFPITAIASILHRVSGVITFVAVGILLWLLGTSLSSPEGFEQASAIMGSFFVKFIMWGILTALAYHVVVGIRHMMMDFGYLEETFEAGKRSAKISFVITVVLSLLAGVLVW

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/5cfdc8e53af69c25ea16ae6c/pdb.gz

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The Resolver thinks Pdb

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Time for openFile(/file/5cfdc8e53af69c25ea16ae6c/pdb.gz): 1139 ms

reading 122 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

122 atoms created

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

Time for creating model: 17 ms

Adding embedded #jmolscript: select ({0:121});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	122
sequence length	122
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	2wdrC00

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

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

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

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations