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


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