1NMPA

Structural genomics, ybgi protein, unknown function
Total Genus 95
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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
95
sequence length
247
structure length
247
Chain Sequence
MKNTELEQLINEKLNSAAISDYAPNGLQVEGKETVQKIVTGVTASQALLDEAVRLGADAVIVHHGYFWKGESPVIRGMKRNRLKTLLANDINLYGWHLPLDAHPELGNNAQLAALLGITVMGEIEPLVPWGELTMPVPGLELASWIEARLGRKPLWCGDTGPEVVQRVAWCTGGGQSFIDSAARFGVDAFITGEVSEQTIHSAREQGLHFYAAGHHATERGGIRALSEWLNENTDLDVTFIDIPNPA
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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 Hypothetical protein ybgI
publication title Crystal Structure of Escherichia coli Protein ybgI, a toroidal structure with a dinuclear metal site
pubmed doi rcsb
source organism Escherichia coli, escherichia coli o157:h7
molecule tags Structural genomics, unknown function
total genus 95
structure length 247
sequence length 247
chains with identical sequence B, C, D, E, F
ec nomenclature
pdb deposition date 2003-01-10

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF01784 NIF3 NIF3 (NGG1p interacting factor 3)
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 1nmpA02
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 1nmpA01
4IWMA 4IWGA 3WSGA 2FYWA 3WSHA 1NMPA 2YYBA 1NMOA 3WSFA 3WSDA 3WSEA 3WSIA
chains in the Genus database with same CATH superfamily
3ZL8A 2IU9A 3L31A 3ZM5A 2AM1A 1NMOA 4IHGA 2IUAA 3WSDA 3WSEA 3ZM6A 3WSGA 4QF5A 4CVLA 3WSHA 4IHHA 1E8CA 3PMOA 4BUBA 2IU8A 4IHFA 3WSIA 2AM2A 3EEQA 4C13A 4CVKA 3WSFA 4E75A 1KO7A 4IWMA 4QDIA 4IWGA 3L2BA 2FYWA 4ZIYA 1KNXA 2IOJA 1NMPA 2WTZA 2YYBA 4C12A 2XJAA 4CVMA 4E79A 1GG4A 3EH0A
chains in the Genus database with same CATH topology
4IWMA 4IWGA 3WSGA 2FYWA 3WSHA 1NMPA 2YYBA 1NMOA 3WSFA 3WSDA 3WSEA 3WSIA
chains in the Genus database with same CATH homology


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