1R8GA

Structure and function of ybdk
Total Genus 105
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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
105
sequence length
368
structure length
352
Chain Sequence
LPDFHVSEPFTLGIELEMQVVNPPGYDLSQDSSMLIDAVKNKITAGEVKHDITESMLELATDVCRDINQAAGQFSAMQKVVLQAATDHHLEICGGGTHPFQKWNFGYLIQQATVFGQHVHVGCASGDDAIYLLHGLSRFVPHFIALSAASPYMQGTDTRFASSRPNIFSAFPDNGPMPWVSNWQQFEALFRCLSYTTMIDSIKDLHWDIRPSPHFGTVEVRVMDTPLTLSHAVNMAGLIQATAHWLLTERPFKHQEKDYLLYKFNRFQACRYGLEGVITDPHTGDRRPLTEDTLRLLEKIAPSAHKIGASSAIEALHRQVVSGLNEAQLMRDFVADGGSLIGLVKKHCEIWA
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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 YbdK is a carboxylate-amine ligase with a gamma-glutamyl:Cysteine ligase activity: crystal structure and enzymatic assays
pubmed doi rcsb
source organism Escherichia coli
molecule tags Ligase
molecule keywords Hypothetical protein ybdK
total genus 105
structure length 352
sequence length 368
chains with identical sequence B
ec nomenclature ec 6.3.2.2: Glutamate--cysteine ligase.
pdb deposition date 2003-10-24

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF04107 GCS2 Glutamate-cysteine ligase family 2(GCS2)
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
3.30.590.20 Alpha Beta 2-Layer Sandwich Creatine Kinase; Chain A, domain 2 Creatine Kinase; Chain A, domain 2 1r8gA00
1TT4A 2D33A 3LN7A 1VA6A 1R8GA 3LN6A 2GWCA 2GWDA 1V4GA 2D32A 3NZTA
chains in the Genus database with same CATH superfamily
4HPPA 4Q2RA 3NZTA 2D33A 4LNIA 4BG4B 2OJWA 1M15A 3NG0A 1HTOA 3L2DA 1I0EA 4BHLA 4AM1A 4RF7A 1V4GA 1F52A 4BG4A 1VRPA 3LN7A 3LVVA 4XYCA 3IG5A 1HTQA 2D3AA 3M10A 1G0WA 2UU7A 4RF9A 2GWCA 3L2EB 4LNOA 1BG0A 1RL9A 1VA6A 3LVWA 1QH4A 4GW0A 5J9AA 1R8GA 1FPYA 1P52A 3FKYA 2QC8A 3ZXRA 3JU6A 4GVZA 3B6RA 1SD0A 1F1HA 1QK1A 4LNNA 3IG8A 2GWDA 1CRKA 4GVYA 3JU5A 1U6RA 5J99A 4S0RA 2D32A 2D3BA 1TT4A 4RF6A 4Z9MA 4LNKA 2GLSA 4GW2A 2J1QA 3DRBA 3JPZA 2D3CA 4S17A 2WGSA 2CRKA 4RF8A 3DREA 3ZXVA 2LGSA 1P50A 3LN6A 3L2EA 2BVCA 3JQ3A 4LNFA 1LGRA 4ACFA 4BAXA 2WHIA
chains in the Genus database with same CATH topology
2QC8A 2D3AA 2D3CA 3NZTA 2D33A 2UU7A 2OJWA 3IG8A 2GWCA 2GWDA 1VA6A 3LVWA 3LN6A 1V4GA 2D32A 2D3BA 1TT4A 3LN7A 3LVVA 1R8GA 3IG5A 4BAXA 3FKYA
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 1TT4 A;  2D33 A;  3LN7 A;  1VA6 A;  1R8G A;  3LN6 A;  2GWC A;  2GWD A;  1V4G A;  2D32 A;  3NZT A; 
#chains in the Genus database with same CATH topology
 4HPP A;  4Q2R A;  3NZT A;  2D33 A;  4LNI A;  4BG4 B;  2OJW A;  1M15 A;  3NG0 A;  1HTO A;  3L2D A;  1I0E A;  4BHL A;  4AM1 A;  4RF7 A;  1V4G A;  1F52 A;  4BG4 A;  1VRP A;  3LN7 A;  3LVV A;  4XYC A;  3IG5 A;  1HTQ A;  2D3A A;  3M10 A;  1G0W A;  2UU7 A;  4RF9 A;  2GWC A;  3L2E B;  4LNO A;  1BG0 A;  1RL9 A;  1VA6 A;  3LVW A;  1QH4 A;  4GW0 A;  5J9A A;  1R8G A;  1FPY A;  1P52 A;  3FKY A;  2QC8 A;  3ZXR A;  3JU6 A;  4GVZ A;  3B6R A;  1SD0 A;  1F1H A;  1QK1 A;  4LNN A;  3IG8 A;  2GWD A;  1CRK A;  4GVY A;  3JU5 A;  1U6R A;  5J99 A;  4S0R A;  2D32 A;  2D3B A;  1TT4 A;  4RF6 A;  4Z9M A;  4LNK A;  2GLS A;  4GW2 A;  2J1Q A;  3DRB A;  3JPZ A;  2D3C A;  4S17 A;  2WGS A;  2CRK A;  4RF8 A;  3DRE A;  3ZXV A;  2LGS A;  1P50 A;  3LN6 A;  3L2E A;  2BVC A;  3JQ3 A;  4LNF A;  1LGR A;  4ACF A;  4BAX A;  2WHI A; 
#chains in the Genus database with same CATH homology
 2QC8 A;  2D3A A;  2D3C A;  3NZT A;  2D33 A;  2UU7 A;  2OJW A;  3IG8 A;  2GWC A;  2GWD A;  1VA6 A;  3LVW A;  3LN6 A;  1V4G A;  2D32 A;  2D3B A;  1TT4 A;  3LN7 A;  3LVV A;  1R8G A;  3IG5 A;  4BAX A;  3FKY 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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