1YBDA

Crystal structure analysis of uridylate kinase from neisseria meningitidis
Total Genus 70
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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
70
sequence length
236
structure length
236
Chain Sequence
QIKYKRVLLKLSGESLMGSDPFGINHDTIVQTVGEIAEVVKMGVQVGIVVGGGNIFRGVSAQAGSMDRATADYMGMMATVMNALALKDAFETLGIKARVQSALSMQQIAETYARPKAIQYLEEGKVVIFAAGTGNPFFTTDTAAALRGAEMNCDVMLKATNVDGVYTADPKKDPSATRYETITFDEALLKNLKVMDATAFALCRERKLNIVVFGIAKEGSLKRVITGEDEGTLVHC
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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 Crystal structure analysis of uridylate kinase from Neisseria meningitidis
rcsb
source organism Neisseria meningitidis
molecule tags Transferase
molecule keywords Uridylate kinase
total genus 70
structure length 236
sequence length 236
chains with identical sequence B, C
ec nomenclature ec 2.7.4.22: UMP kinase.
pdb deposition date 2004-12-20

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 1ybdA00
3D2PA 3ZZIA 1GS5A 2JJXA 3K4OA 3B8GA 2CDQA 3WWMA 3S6HA 2R98A 3AAWA 4F6TA 3K52A 3TVIA 4I49A 3ZZGA 4JZ8A 2J4JA 4NDRB 1OHBA 4NDPB 3WWNA 2BUFA 2A1FA 4NDOA 3KZFA 3ZZHA 4NDQB 1B7BA 2AP9A 2WXBA 2BRXA 2RD5A 4NDQA 2J5TA 2E9YA 3LKKA 4JZ9A 4AXSA 1GSJA 3S6GA 4AB7A 3LL5A 3AB4A 2JI5A 3D40A 4Q1TA 3S6KA 4A7WA 2BNFA 3C1NA 3D2MA 3EK5A 3K4YA 4USJA 3QVHA 1OH9A 3U6UA 2BNEA 1OHAA 3L76A 1Z9DA 2J4LA 4NDOB 3QUOA 4F6TB 3C1MA 3T7BA 2BRIA 2W21A 2WE5A 2J0XA 3AB2A 4OLCA 3ZZFA 2OGXB 2J5VA 2HMFA 2V5HA 3NWYA 3K56A 4JZ7A 2J4KA 4NDRA 1E19A 2AKOA 3EK6A 2BNDA 3QURA 3D41A 4KZTA 2IJ9A 2R8VA 4A7XA 1YBDA 3QVFA 2VA1A 3C20A 3LL9A 2BTYA 2J0WA 3QUNA 2WE4A 2JJ4A 2OGXA 2V4YA 3L86A 4NDPA 2X2WA 2BMUA
chains in the Genus database with same CATH superfamily
3D2PA 3ZZIA 1GS5A 2JJXA 3K4OA 3B8GA 2CDQA 3WWMA 3S6HA 2R98A 3AAWA 4F6TA 3K52A 3TVIA 4I49A 3ZZGA 4JZ8A 2J4JA 4NDRB 1OHBA 4NDPB 3WWNA 2BUFA 2A1FA 4NDOA 3KZFA 3ZZHA 4NDQB 1B7BA 2AP9A 2WXBA 2BRXA 2RD5A 4NDQA 2J5TA 2E9YA 3LKKA 4JZ9A 4AXSA 1GSJA 3S6GA 4AB7A 3LL5A 3AB4A 2JI5A 3D40A 4Q1TA 3S6KA 4A7WA 2BNFA 3C1NA 3D2MA 3EK5A 3K4YA 4USJA 3QVHA 1OH9A 3U6UA 2BNEA 1OHAA 3L76A 1Z9DA 2J4LA 4NDOB 3QUOA 4F6TB 3C1MA 3T7BA 2BRIA 2W21A 2WE5A 2J0XA 3AB2A 4OLCA 3ZZFA 2OGXB 2J5VA 2HMFA 2V5HA 3NWYA 3K56A 4JZ7A 2J4KA 4NDRA 1E19A 2AKOA 3EK6A 2BNDA 3QURA 3D41A 4KZTA 2IJ9A 2R8VA 4A7XA 1YBDA 3QVFA 2VA1A 3C20A 3LL9A 2BTYA 2J0WA 3QUNA 2WE4A 2JJ4A 2OGXA 2V4YA 3L86A 4NDPA 2X2WA 2BMUA
chains in the Genus database with same CATH topology
3D2PA 3ZZIA 1GS5A 2JJXA 3K4OA 3B8GA 2CDQA 3WWMA 3S6HA 2R98A 3AAWA 4F6TA 3K52A 3TVIA 4I49A 3ZZGA 4JZ8A 2J4JA 4NDRB 1OHBA 4NDPB 3WWNA 2BUFA 2A1FA 4NDOA 3KZFA 3ZZHA 4NDQB 1B7BA 2AP9A 2WXBA 2BRXA 2RD5A 4NDQA 2J5TA 2E9YA 3LKKA 4JZ9A 4AXSA 1GSJA 3S6GA 4AB7A 3LL5A 3AB4A 2JI5A 3D40A 4Q1TA 3S6KA 4A7WA 2BNFA 3C1NA 3D2MA 3EK5A 3K4YA 4USJA 3QVHA 1OH9A 3U6UA 2BNEA 1OHAA 3L76A 1Z9DA 2J4LA 4NDOB 3QUOA 4F6TB 3C1MA 3T7BA 2BRIA 2W21A 2WE5A 2J0XA 3AB2A 4OLCA 3ZZFA 2OGXB 2J5VA 2HMFA 2V5HA 3NWYA 3K56A 4JZ7A 2J4KA 4NDRA 1E19A 2AKOA 3EK6A 2BNDA 3QURA 3D41A 4KZTA 2IJ9A 2R8VA 4A7XA 1YBDA 3QVFA 2VA1A 3C20A 3LL9A 2BTYA 2J0WA 3QUNA 2WE4A 2JJ4A 2OGXA 2V4YA 3L86A 4NDPA 2X2WA 2BMUA
chains in the Genus database with same CATH homology


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