2VA1A

Crystal structure of ump kinase from ureaplasma parvum
Total Genus 81
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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
81
sequence length
234
structure length
226
Chain Sequence
RKQRIVIKISGACLKQNDSSIIDFIKINDLAEQIEKISKKYIVSIVLGGGNIWRGSIAKELDMDRNLADNMGMMATIINGLALENALNHLNVNTIVLSAIKCDKLVHESSANNIKKAIEKEQVMIFVAGTGFPYFTTDSCAAIRAAETESSIILMGKNGVDGVYDSDFYEHITFNMALTQNLKVMDATALALCQENNINLLVFNIDKPNAIVDVLEKKNKYTIVSK
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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.


  Genus data interpretation
Chord Diagram
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publication title Structural and Functional Investigations of Ureaplasma Parvum Ump Kinase - a Potential Antibacterial Drug Target
pubmed doi rcsb
molecule keywords URIDYLATE KINASE
molecule tags Transferase
source organism Ureaplasma parvum
total genus 81
structure length 226
sequence length 234
chains with identical sequence B, C, D, E, F
ec nomenclature ec 2.7.4.22: UMP kinase.
pdb deposition date 2007-08-28

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF00696 AA_kinase Amino acid kinase family
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
3.40.1160.10 Alpha Beta 3-Layer(aba) Sandwich Carbamate kinase Acetylglutamate kinase-like 2va1A00
4A7XA 2AP9A 3KZFA 1OH9A 2V5HA 2WE5A 3AB4A 3QVFA 2AKOA 3S6KA 2BNDA 3K56A 2E9YA 4AXSA 2RD5A 2R98A 2J0WA 2JJ4A 3L86A 3QURA 3D41A 3QUOA 2V4YA 3L76A 2J4KA 2BTYA 2J0XA 3LL5A 4AB7A 4NDPA 2BNEA 4NDQA 3T7BA 2BNFA 3S6GA 1GS5A 2BUFA 2HMFA 3EK6A 4Q1TA 2OGXA 2J4JA 2J4LA 3ZZGA 3B8GA 2X2WA 2IJ9A 2BMUA 3AAWA 2WE4A 3QUNA 3QVHA 3AB2A 3NWYA 2VA1A 2JI5A 2W21A 3S6HA 4NDRA 3ZZIA 2CDQA 3K4OA 2R8VA 4NDPB 4NDQB 1E19A 4JZ9A 3D40A 3K4YA 3WWNA 2JJXA 2OGXB 3D2PA 3TVIA 2BRXA 3C1MA 1YBDA 1Z9DA 1GSJA 4JZ8A 2J5TA 3K52A 3LL9A 4F6TA 3ZZHA 4F6TB 3C20A 3D2MA 4JZ7A 3C1NA 2BRIA 4NDRB 3U6UA 2WXBA 2J5VA 2A1FA 3ZZFA 3EK5A 3LKKA 4OLCA 3WWMA 4USJA 1OHAA 4NDOA 1B7BA 4KZTA 1OHBA 4NDOB 4A7WA 4I49A
chains in the Genus database with same CATH superfamily
4A7XA 2AP9A 3KZFA 1OH9A 2V5HA 2WE5A 3AB4A 3QVFA 2AKOA 3S6KA 2BNDA 3K56A 2E9YA 4AXSA 2RD5A 2R98A 2J0WA 2JJ4A 3L86A 3QURA 3D41A 3QUOA 2V4YA 3L76A 2J4KA 2BTYA 2J0XA 3LL5A 4AB7A 4NDPA 2BNEA 4NDQA 3T7BA 2BNFA 3S6GA 1GS5A 2BUFA 2HMFA 3EK6A 4Q1TA 2OGXA 2J4JA 2J4LA 3ZZGA 3B8GA 2X2WA 2IJ9A 2BMUA 3AAWA 2WE4A 3QUNA 3QVHA 3AB2A 3NWYA 2VA1A 2JI5A 2W21A 3S6HA 4NDRA 3ZZIA 2CDQA 3K4OA 2R8VA 4NDPB 4NDQB 1E19A 4JZ9A 3D40A 3K4YA 3WWNA 2JJXA 2OGXB 3D2PA 3TVIA 2BRXA 3C1MA 1YBDA 1Z9DA 1GSJA 4JZ8A 2J5TA 3K52A 3LL9A 4F6TA 3ZZHA 4F6TB 3C20A 3D2MA 4JZ7A 3C1NA 2BRIA 4NDRB 3U6UA 2WXBA 2J5VA 2A1FA 3ZZFA 3EK5A 3LKKA 4OLCA 3WWMA 4USJA 1OHAA 4NDOA 1B7BA 4KZTA 1OHBA 4NDOB 4A7WA 4I49A
chains in the Genus database with same CATH topology
4A7XA 2AP9A 3KZFA 1OH9A 2V5HA 2WE5A 3AB4A 3QVFA 2AKOA 3S6KA 2BNDA 3K56A 2E9YA 4AXSA 2RD5A 2R98A 2J0WA 2JJ4A 3L86A 3QURA 3D41A 3QUOA 2V4YA 3L76A 2J4KA 2BTYA 2J0XA 3LL5A 4AB7A 4NDPA 2BNEA 4NDQA 3T7BA 2BNFA 3S6GA 1GS5A 2BUFA 2HMFA 3EK6A 4Q1TA 2OGXA 2J4JA 2J4LA 3ZZGA 3B8GA 2X2WA 2IJ9A 2BMUA 3AAWA 2WE4A 3QUNA 3QVHA 3AB2A 3NWYA 2VA1A 2JI5A 2W21A 3S6HA 4NDRA 3ZZIA 2CDQA 3K4OA 2R8VA 4NDPB 4NDQB 1E19A 4JZ9A 3D40A 3K4YA 3WWNA 2JJXA 2OGXB 3D2PA 3TVIA 2BRXA 3C1MA 1YBDA 1Z9DA 1GSJA 4JZ8A 2J5TA 3K52A 3LL9A 4F6TA 3ZZHA 4F6TB 3C20A 3D2MA 4JZ7A 3C1NA 2BRIA 4NDRB 3U6UA 2WXBA 2J5VA 2A1FA 3ZZFA 3EK5A 3LKKA 4OLCA 3WWMA 4USJA 1OHAA 4NDOA 1B7BA 4KZTA 1OHBA 4NDOB 4A7WA 4I49A
chains in the Genus database with same CATH homology

  
#chains in the Genus database with same CATH superfamily
 4A7X A;  2AP9 A;  3KZF A;  1OH9 A;  2V5H A;  2WE5 A;  3AB4 A;  3QVF A;  2AKO A;  3S6K A;  2BND A;  3K56 A;  2E9Y A;  4AXS A;  2RD5 A;  2R98 A;  2J0W A;  2JJ4 A;  3L86 A;  3QUR A;  3D41 A;  3QUO A;  2V4Y A;  3L76 A;  2J4K A;  2BTY A;  2J0X A;  3LL5 A;  4AB7 A;  4NDP A;  2BNE A;  4NDQ A;  3T7B A;  2BNF A;  3S6G A;  1GS5 A;  2BUF A;  2HMF A;  3EK6 A;  4Q1T A;  2OGX A;  2J4J A;  2J4L A;  3ZZG A;  3B8G A;  2X2W A;  2IJ9 A;  2BMU A;  3AAW A;  2WE4 A;  3QUN A;  3QVH A;  3AB2 A;  3NWY A;  2VA1 A;  2JI5 A;  2W21 A;  3S6H A;  4NDR A;  3ZZI A;  2CDQ A;  3K4O A;  2R8V A;  4NDP B;  4NDQ B;  1E19 A;  4JZ9 A;  3D40 A;  3K4Y A;  3WWN A;  2JJX A;  2OGX B;  3D2P A;  3TVI A;  2BRX A;  3C1M A;  1YBD A;  1Z9D A;  1GSJ A;  4JZ8 A;  2J5T A;  3K52 A;  3LL9 A;  4F6T A;  3ZZH A;  4F6T B;  3C20 A;  3D2M A;  4JZ7 A;  3C1N A;  2BRI A;  4NDR B;  3U6U A;  2WXB A;  2J5V A;  2A1F A;  3ZZF A;  3EK5 A;  3LKK A;  4OLC A;  3WWM A;  4USJ A;  1OHA A;  4NDO A;  1B7B A;  4KZT A;  1OHB A;  4NDO B;  4A7W A;  4I49 A; 
#chains in the Genus database with same CATH topology
 4A7X A;  2AP9 A;  3KZF A;  1OH9 A;  2V5H A;  2WE5 A;  3AB4 A;  3QVF A;  2AKO A;  3S6K A;  2BND A;  3K56 A;  2E9Y A;  4AXS A;  2RD5 A;  2R98 A;  2J0W A;  2JJ4 A;  3L86 A;  3QUR A;  3D41 A;  3QUO A;  2V4Y A;  3L76 A;  2J4K A;  2BTY A;  2J0X A;  3LL5 A;  4AB7 A;  4NDP A;  2BNE A;  4NDQ A;  3T7B A;  2BNF A;  3S6G A;  1GS5 A;  2BUF A;  2HMF A;  3EK6 A;  4Q1T A;  2OGX A;  2J4J A;  2J4L A;  3ZZG A;  3B8G A;  2X2W A;  2IJ9 A;  2BMU A;  3AAW A;  2WE4 A;  3QUN A;  3QVH A;  3AB2 A;  3NWY A;  2VA1 A;  2JI5 A;  2W21 A;  3S6H A;  4NDR A;  3ZZI A;  2CDQ A;  3K4O A;  2R8V A;  4NDP B;  4NDQ B;  1E19 A;  4JZ9 A;  3D40 A;  3K4Y A;  3WWN A;  2JJX A;  2OGX B;  3D2P A;  3TVI A;  2BRX A;  3C1M A;  1YBD A;  1Z9D A;  1GSJ A;  4JZ8 A;  2J5T A;  3K52 A;  3LL9 A;  4F6T A;  3ZZH A;  4F6T B;  3C20 A;  3D2M A;  4JZ7 A;  3C1N A;  2BRI A;  4NDR B;  3U6U A;  2WXB A;  2J5V A;  2A1F A;  3ZZF A;  3EK5 A;  3LKK A;  4OLC A;  3WWM A;  4USJ A;  1OHA A;  4NDO A;  1B7B A;  4KZT A;  1OHB A;  4NDO B;  4A7W A;  4I49 A; 
#chains in the Genus database with same CATH homology
 4A7X A;  2AP9 A;  3KZF A;  1OH9 A;  2V5H A;  2WE5 A;  3AB4 A;  3QVF A;  2AKO A;  3S6K A;  2BND A;  3K56 A;  2E9Y A;  4AXS A;  2RD5 A;  2R98 A;  2J0W A;  2JJ4 A;  3L86 A;  3QUR A;  3D41 A;  3QUO A;  2V4Y A;  3L76 A;  2J4K A;  2BTY A;  2J0X A;  3LL5 A;  4AB7 A;  4NDP A;  2BNE A;  4NDQ A;  3T7B A;  2BNF A;  3S6G A;  1GS5 A;  2BUF A;  2HMF A;  3EK6 A;  4Q1T A;  2OGX A;  2J4J A;  2J4L A;  3ZZG A;  3B8G A;  2X2W A;  2IJ9 A;  2BMU A;  3AAW A;  2WE4 A;  3QUN A;  3QVH A;  3AB2 A;  3NWY A;  2VA1 A;  2JI5 A;  2W21 A;  3S6H A;  4NDR A;  3ZZI A;  2CDQ A;  3K4O A;  2R8V A;  4NDP B;  4NDQ B;  1E19 A;  4JZ9 A;  3D40 A;  3K4Y A;  3WWN A;  2JJX A;  2OGX B;  3D2P A;  3TVI A;  2BRX A;  3C1M A;  1YBD A;  1Z9D A;  1GSJ A;  4JZ8 A;  2J5T A;  3K52 A;  3LL9 A;  4F6T A;  3ZZH A;  4F6T B;  3C20 A;  3D2M A;  4JZ7 A;  3C1N A;  2BRI A;  4NDR B;  3U6U A;  2WXB A;  2J5V A;  2A1F A;  3ZZF A;  3EK5 A;  3LKK A;  4OLC A;  3WWM A;  4USJ A;  1OHA A;  4NDO A;  1B7B A;  4KZT A;  1OHB A;  4NDO B;  4A7W A;  4I49 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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