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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molecule keywords Putative GTP cyclohydrolase 1 type 2
publication title A possible iron delivery function of the dinuclear iron center of HcgD in [Fe]-hydrogenase cofactor biosynthesis
pubmed doi rcsb
source organism Methanocaldococcus jannaschii
molecule tags Metal binding protein
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
3WSIA 4IWGA 1NMOA 3WSFA 2FYWA 1NMPA 4IWMA 3WSEA 3WSDA 2YYBA 3WSGA 3WSHA
chains in the Genus database with same CATH superfamily
3WSIA 1NMOA 3L2BA 4QF5A 2IU8A 2IOJA 4CVLA 2YYBA 3EH0A 4QDIA 4E79A 3WSGA 3WSHA 4C12A 4ZIYA 4IHFA 1NMPA 2FYWA 3ZM5A 4IHHA 3WSEA 4E75A 1KNXA 3WSDA 4CVMA 4C13A 3ZL8A 4IHGA 3WSFA 1E8CA 2WTZA 4IWMA 3L31A 3EEQA 2AM2A 3ZM6A 2XJAA 1KO7A 2IU9A 4IWGA 2AM1A 2IUAA 4BUBA 1GG4A 3PMOA 4CVKA
chains in the Genus database with same CATH topology
3WSIA 4IWGA 1NMOA 3WSFA 2FYWA 1NMPA 4IWMA 3WSEA 3WSDA 2YYBA 3WSGA 3WSHA
chains in the Genus database with same CATH homology


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