2Y8NB

Crystal structure of glycyl radical enzyme
Total Genus 18
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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
18
sequence length
86
structure length
86
Chain Sequence
MRHYDCKNYINLDCEKGLCALTKGMVPIDGEGSEACPNFKPAEKCGNCKNFCNPDKYGLGTCTGLEKENWAYATCGASACPSYKAE
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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 4-HYDROXYPHENYLACETATE DECARBOXYLASE LARGE SUBUNIT
publication title Structural Basis for a Kolbe-Type Decarboxylation Catalyzed by a Glycyl Radical Enzyme.
pubmed doi rcsb
source organism Clostridium scatologenes
molecule tags Lyase
total genus 18
structure length 86
sequence length 86
chains with identical sequence D
ec nomenclature ec 4.1.1.83: 4-hydroxyphenylacetate decarboxylase.
pdb deposition date 2011-02-08

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
B PF18524 HPIP_like High potential iron-sulfur protein like
B PF18671 4HPAD_g_N 4-Hydroxyphenylacetate decarboxylase subunit gamma N-terminal
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
2.20.70.100 Mainly Beta Single Sheet Ubiquitin Ligase Nedd4; Chain: W; Ubiquitin Ligase Nedd4; Chain: W; 2y8nB01
2.20.70.100 Mainly Beta Single Sheet Ubiquitin Ligase Nedd4; Chain: W; Ubiquitin Ligase Nedd4; Chain: W; 2y8nB02
2Y8NB 2YAJB
chains in the Genus database with same CATH superfamily
2E45A 3M85A 2XP4A 2ZQSA 2ZR4A 3LKXA 1RP5A 2M3OW 2EZ5W 2DJYA 4A0TA 1JMQA 1TR8A 2F21A 3KAHA 3MCBB 2ITKA 2XPAA 2XP8A 4U86A 3FSBA 2M8JA 2YSIA 1FLCA 2DK1A 3LKXB 3KADA 3MQGA 3FSCA 2XP5A 3KCEA 3TDBA 2JMFA 3NTPA 5E62A 2L4JA 2LAJA 3KAFA 5U47A 1PINA 2DK7A 2YAJB 3L4HA 2OWOA 2DWVA 1TK7A 2M8IA 2XPBA 3KAIA 2MDIA 2XP3A 2WAEA 2Q5AA 2XP9A 2KXQA 1O6WA 3KABA 4QIBA 5E65A 2Y8NB 2JV4A 4REXA 3M7NA 1WR7A 5E64A 2YSBA 4U85A 3PQHA 1EG4A 2QRVA 3WH0A 3ODKA 1YW5A 1I5HW 2ZQTA 2ZQVA 2ZR5A 3KAGA 4GLXA 2BA1A 2JXWA 3TCZA 1K9QA 3FS8A 4E5RA 2ZQUA 5E5WA 1NMVA 1EG3A 2DMVA 2YSHA 2ZAJA 3CNGA 4U84A 3LE4A 1F8AB 2RE3A 2ZR6A 2JX8A 2XP7A 3TC5A 2YSFA 5E66A 1K9RA 5AHTA 5CQ2A 3MQHA 2YSGA 4A0UA 2XP6A 3MCBA 3OOBA 1WMVA 2WADA 1ZCNA
chains in the Genus database with same CATH topology
2E45A 3M85A 2XP4A 2ZQSA 2ZR4A 3LKXA 1RP5A 2M3OW 2EZ5W 2DJYA 4A0TA 1JMQA 1TR8A 2F21A 3KAHA 3MCBB 2ITKA 2XPAA 2XP8A 4U86A 3FSBA 2M8JA 2YSIA 1FLCA 2DK1A 3LKXB 3KADA 3MQGA 3FSCA 2XP5A 3KCEA 3TDBA 2JMFA 3NTPA 5E62A 2L4JA 2LAJA 3KAFA 5U47A 1PINA 2DK7A 2YAJB 3L4HA 2OWOA 2DWVA 1TK7A 2M8IA 2XPBA 3KAIA 2MDIA 2XP3A 2WAEA 2Q5AA 2XP9A 2KXQA 1O6WA 3KABA 4QIBA 5E65A 2Y8NB 2JV4A 4REXA 3M7NA 1WR7A 5E64A 2YSBA 4U85A 3PQHA 1EG4A 2QRVA 3WH0A 3ODKA 1YW5A 1I5HW 2ZQTA 2ZQVA 2ZR5A 3KAGA 4GLXA 2BA1A 2JXWA 3TCZA 1K9QA 3FS8A 4E5RA 2ZQUA 5E5WA 1NMVA 1EG3A 2DMVA 2YSHA 2ZAJA 3CNGA 4U84A 3LE4A 1F8AB 2RE3A 2ZR6A 2JX8A 2XP7A 3TC5A 2YSFA 5E66A 1K9RA 5AHTA 5CQ2A 3MQHA 2YSGA 4A0UA 2XP6A 3MCBA 3OOBA 1WMVA 2WADA 1ZCNA
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 2Y8N B;  2YAJ B; 
#chains in the Genus database with same CATH topology
 2E45 A;  3M85 A;  2XP4 A;  2ZQS A;  2ZR4 A;  3LKX A;  1RP5 A;  2M3O W;  2EZ5 W;  2DJY A;  4A0T A;  1JMQ A;  1TR8 A;  2F21 A;  3KAH A;  3MCB B;  2ITK A;  2XPA A;  2XP8 A;  4U86 A;  3FSB A;  2M8J A;  2YSI A;  1FLC A;  2DK1 A;  3LKX B;  3KAD A;  3MQG A;  3FSC A;  2XP5 A;  3KCE A;  3TDB A;  2JMF A;  3NTP A;  5E62 A;  2L4J A;  2LAJ A;  3KAF A;  5U47 A;  1PIN A;  2DK7 A;  2YAJ B;  3L4H A;  2OWO A;  2DWV A;  1TK7 A;  2M8I A;  2XPB A;  3KAI A;  2MDI A;  2XP3 A;  2WAE A;  2Q5A A;  2XP9 A;  2KXQ A;  1O6W A;  3KAB A;  4QIB A;  5E65 A;  2Y8N B;  2JV4 A;  4REX A;  3M7N A;  1WR7 A;  5E64 A;  2YSB A;  4U85 A;  3PQH A;  1EG4 A;  2QRV A;  3WH0 A;  3ODK A;  1YW5 A;  1I5H W;  2ZQT A;  2ZQV A;  2ZR5 A;  3KAG A;  4GLX A;  2BA1 A;  2JXW A;  3TCZ A;  1K9Q A;  3FS8 A;  4E5R A;  2ZQU A;  5E5W A;  1NMV A;  1EG3 A;  2DMV A;  2YSH A;  2ZAJ A;  3CNG A;  4U84 A;  3LE4 A;  1F8A B;  2RE3 A;  2ZR6 A;  2JX8 A;  2XP7 A;  3TC5 A;  2YSF A;  5E66 A;  1K9R A;  5AHT A;  5CQ2 A;  3MQH A;  2YSG A;  4A0U A;  2XP6 A;  3MCB A;  3OOB A;  1WMV A;  2WAD A;  1ZCN A; 
#chains in the Genus database with same CATH homology
 2E45 A;  3M85 A;  2XP4 A;  2ZQS A;  2ZR4 A;  3LKX A;  1RP5 A;  2M3O W;  2EZ5 W;  2DJY A;  4A0T A;  1JMQ A;  1TR8 A;  2F21 A;  3KAH A;  3MCB B;  2ITK A;  2XPA A;  2XP8 A;  4U86 A;  3FSB A;  2M8J A;  2YSI A;  1FLC A;  2DK1 A;  3LKX B;  3KAD A;  3MQG A;  3FSC A;  2XP5 A;  3KCE A;  3TDB A;  2JMF A;  3NTP A;  5E62 A;  2L4J A;  2LAJ A;  3KAF A;  5U47 A;  1PIN A;  2DK7 A;  2YAJ B;  3L4H A;  2OWO A;  2DWV A;  1TK7 A;  2M8I A;  2XPB A;  3KAI A;  2MDI A;  2XP3 A;  2WAE A;  2Q5A A;  2XP9 A;  2KXQ A;  1O6W A;  3KAB A;  4QIB A;  5E65 A;  2Y8N B;  2JV4 A;  4REX A;  3M7N A;  1WR7 A;  5E64 A;  2YSB A;  4U85 A;  3PQH A;  1EG4 A;  2QRV A;  3WH0 A;  3ODK A;  1YW5 A;  1I5H W;  2ZQT A;  2ZQV A;  2ZR5 A;  3KAG A;  4GLX A;  2BA1 A;  2JXW A;  3TCZ A;  1K9Q A;  3FS8 A;  4E5R A;  2ZQU A;  5E5W A;  1NMV A;  1EG3 A;  2DMV A;  2YSH A;  2ZAJ A;  3CNG A;  4U84 A;  3LE4 A;  1F8A B;  2RE3 A;  2ZR6 A;  2JX8 A;  2XP7 A;  3TC5 A;  2YSF A;  5E66 A;  1K9R A;  5AHT A;  5CQ2 A;  3MQH A;  2YSG A;  4A0U A;  2XP6 A;  3MCB A;  3OOB A;  1WMV A;  2WAD A;  1ZCN 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)

 
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#similar chains, but unknotted
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