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


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