3WSDA

Oxidized hcgd from methanocaldococcus jannaschii
Total Genus 92
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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
92
sequence length
247
structure length
247
Chain Sequence
VVNMKAKEIIEFIETFAPKDLAIEGDNIGLQVGDNLDKEIKKLGIALDPSLSVIKKAEKEGVDFLFTHHPLLKDPIRNFTGVIYKKLKILMENDIILYSAHTNLDICKNGLNDALAELYNLENPKPLYDNGLGRVGIFKGSFEEFLEITKKYIHKNPIVVKSKEVDDNFKLAVLSGYGLSQSSIKYVAEKADVYLSGDLTHHSKILAEELGLVVVDATHYSTEVFGLKKFKEFLSSNLDLEIISLDF
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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

After clicking on a point (x,y) in the genus matrix above, a subchain from x to y is shown in color.

Chord Diagram
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publication title A possible iron delivery function of the dinuclear iron center of HcgD in [Fe]-hydrogenase cofactor biosynthesis
pubmed doi rcsb
molecule tags Metal binding protein
source organism Methanocaldococcus jannaschii
molecule keywords Putative GTP cyclohydrolase 1 type 2
total genus 92
structure length 247
sequence length 247
chains with identical sequence B, C, D, E, F
ec nomenclature
pdb deposition date 2014-03-13
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
3.40.1390.30 Alpha Beta 3-Layer(aba) Sandwich Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1 NIF3 (NGG1p interacting factor 3)-like 3wsdA01
3.40.1390.30 Alpha Beta 3-Layer(aba) Sandwich Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1 NIF3 (NGG1p interacting factor 3)-like 3wsdA02
4IWMA 3WSHA 1NMPA 3WSGA 2FYWA 3WSFA 3WSDA 2YYBA 3WSIA 1NMOA 4IWGA 3WSEA
chains in the Genus database with same CATH superfamily
4IWMA 4C13A 3WSGA 2IUAA 2YYBA 3WSEA 2IU8A 4IHGA 3WSDA 3ZL8A 4QF5A 4E75A 2WTZA 3L2BA 2XJAA 4BUBA 1NMPA 4E79A 2FYWA 3L31A 3WSFA 2IU9A 4CVMA 1KO7A 3EH0A 2AM1A 3WSIA 3ZM5A 4CVLA 4IWGA 1E8CA 4QDIA 4ZIYA 3ZM6A 4C12A 3WSHA 1GG4A 4IHHA 4CVKA 3PMOA 4IHFA 1KNXA 3EEQA 1NMOA 2IOJA 2AM2A
chains in the Genus database with same CATH topology
4IWMA 3WSHA 1NMPA 3WSGA 2FYWA 3WSFA 3WSDA 2YYBA 3WSIA 1NMOA 4IWGA 3WSEA
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 4IWM A;  3WSH A;  1NMP A;  3WSG A;  2FYW A;  3WSF A;  3WSD A;  2YYB A;  3WSI A;  1NMO A;  4IWG A;  3WSE A; 
#chains in the Genus database with same CATH topology
 4IWM A;  4C13 A;  3WSG A;  2IUA A;  2YYB A;  3WSE A;  2IU8 A;  4IHG A;  3WSD A;  3ZL8 A;  4QF5 A;  4E75 A;  2WTZ A;  3L2B A;  2XJA A;  4BUB A;  1NMP A;  4E79 A;  2FYW A;  3L31 A;  3WSF A;  2IU9 A;  4CVM A;  1KO7 A;  3EH0 A;  2AM1 A;  3WSI A;  3ZM5 A;  4CVL A;  4IWG A;  1E8C A;  4QDI A;  4ZIY A;  3ZM6 A;  4C12 A;  3WSH A;  1GG4 A;  4IHH A;  4CVK A;  3PMO A;  4IHF A;  1KNX A;  3EEQ A;  1NMO A;  2IOJ A;  2AM2 A; 
#chains in the Genus database with same CATH homology
 4IWM A;  3WSH A;  1NMP A;  3WSG A;  2FYW A;  3WSF A;  3WSD A;  2YYB A;  3WSI A;  1NMO A;  4IWG A;  3WSE 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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