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 tags Lyase
source organism Clostridium scatologenes
publication title Structural Basis for a Kolbe-Type Decarboxylation Catalyzed by a Glycyl Radical Enzyme.
pubmed doi rcsb
molecule keywords 4-HYDROXYPHENYLACETATE DECARBOXYLASE LARGE SUBUNIT
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
2XP3A 1PINA 1TR8A 3KCEA 2M3OW 2M8IA 1ZCNA 2ZQSA 2ZR6A 3TCZA 1WR7A 3LKXA 5E62A 1TK7A 2EZ5W 2KXQA 5CQ2A 3KAIA 1EG4A 2DJYA 2XP8A 2ZQVA 3WH0A 3ODKA 2BA1A 2JX8A 4U84A 2YSIA 2XP6A 2XP4A 2ZQUA 2YAJB 2XP7A 2RE3A 3LE4A 3FS8A 5E66A 3KAFA 2E45A 2ZR4A 2WADA 5AHTA 3MQGA 3OOBA 3TC5A 2DMVA 1K9RA 3M7NA 2MDIA 2Y8NB 2XPBA 3LKXB 3FSCA 3M85A 5E64A 1YW5A 3FSBA 3MCBA 2QRVA 5E5WA 1I5HW 1FLCA 2ZAJA 4A0TA 2YSHA 1JMQA 2DK7A 3TDBA 1WMVA 2ZQTA 2YSGA 3KABA 3KAHA 1EG3A 1RP5A 3PQHA 3KADA 3NTPA 2XPAA 3MCBB 2JMFA 2L4JA 2Q5AA 2M8JA 4E5RA 4U85A 2OWOA 2YSFA 3CNGA 5E65A 2JXWA 3L4HA 2ITKA 4A0UA 2DWVA 2YSBA 2XP9A 3MQHA 4GLXA 1F8AB 2F21A 2ZR5A 2DK1A 3KAGA 2XP5A 1NMVA 5U47A 2LAJA 1K9QA 4U86A 2JV4A 4REXA 2WAEA 4QIBA 1O6WA
chains in the Genus database with same CATH topology
2XP3A 1PINA 1TR8A 3KCEA 2M3OW 2M8IA 1ZCNA 2ZQSA 2ZR6A 3TCZA 1WR7A 3LKXA 5E62A 1TK7A 2EZ5W 2KXQA 5CQ2A 3KAIA 1EG4A 2DJYA 2XP8A 2ZQVA 3WH0A 3ODKA 2BA1A 2JX8A 4U84A 2YSIA 2XP6A 2XP4A 2ZQUA 2YAJB 2XP7A 2RE3A 3LE4A 3FS8A 5E66A 3KAFA 2E45A 2ZR4A 2WADA 5AHTA 3MQGA 3OOBA 3TC5A 2DMVA 1K9RA 3M7NA 2MDIA 2Y8NB 2XPBA 3LKXB 3FSCA 3M85A 5E64A 1YW5A 3FSBA 3MCBA 2QRVA 5E5WA 1I5HW 1FLCA 2ZAJA 4A0TA 2YSHA 1JMQA 2DK7A 3TDBA 1WMVA 2ZQTA 2YSGA 3KABA 3KAHA 1EG3A 1RP5A 3PQHA 3KADA 3NTPA 2XPAA 3MCBB 2JMFA 2L4JA 2Q5AA 2M8JA 4E5RA 4U85A 2OWOA 2YSFA 3CNGA 5E65A 2JXWA 3L4HA 2ITKA 4A0UA 2DWVA 2YSBA 2XP9A 3MQHA 4GLXA 1F8AB 2F21A 2ZR5A 2DK1A 3KAGA 2XP5A 1NMVA 5U47A 2LAJA 1K9QA 4U86A 2JV4A 4REXA 2WAEA 4QIBA 1O6WA
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
 2XP3 A;  1PIN A;  1TR8 A;  3KCE A;  2M3O W;  2M8I A;  1ZCN A;  2ZQS A;  2ZR6 A;  3TCZ A;  1WR7 A;  3LKX A;  5E62 A;  1TK7 A;  2EZ5 W;  2KXQ A;  5CQ2 A;  3KAI A;  1EG4 A;  2DJY A;  2XP8 A;  2ZQV A;  3WH0 A;  3ODK A;  2BA1 A;  2JX8 A;  4U84 A;  2YSI A;  2XP6 A;  2XP4 A;  2ZQU A;  2YAJ B;  2XP7 A;  2RE3 A;  3LE4 A;  3FS8 A;  5E66 A;  3KAF A;  2E45 A;  2ZR4 A;  2WAD A;  5AHT A;  3MQG A;  3OOB A;  3TC5 A;  2DMV A;  1K9R A;  3M7N A;  2MDI A;  2Y8N B;  2XPB A;  3LKX B;  3FSC A;  3M85 A;  5E64 A;  1YW5 A;  3FSB A;  3MCB A;  2QRV A;  5E5W A;  1I5H W;  1FLC A;  2ZAJ A;  4A0T A;  2YSH A;  1JMQ A;  2DK7 A;  3TDB A;  1WMV A;  2ZQT A;  2YSG A;  3KAB A;  3KAH A;  1EG3 A;  1RP5 A;  3PQH A;  3KAD A;  3NTP A;  2XPA A;  3MCB B;  2JMF A;  2L4J A;  2Q5A A;  2M8J A;  4E5R A;  4U85 A;  2OWO A;  2YSF A;  3CNG A;  5E65 A;  2JXW A;  3L4H A;  2ITK A;  4A0U A;  2DWV A;  2YSB A;  2XP9 A;  3MQH A;  4GLX A;  1F8A B;  2F21 A;  2ZR5 A;  2DK1 A;  3KAG A;  2XP5 A;  1NMV A;  5U47 A;  2LAJ A;  1K9Q A;  4U86 A;  2JV4 A;  4REX A;  2WAE A;  4QIB A;  1O6W A; 
#chains in the Genus database with same CATH homology
 2XP3 A;  1PIN A;  1TR8 A;  3KCE A;  2M3O W;  2M8I A;  1ZCN A;  2ZQS A;  2ZR6 A;  3TCZ A;  1WR7 A;  3LKX A;  5E62 A;  1TK7 A;  2EZ5 W;  2KXQ A;  5CQ2 A;  3KAI A;  1EG4 A;  2DJY A;  2XP8 A;  2ZQV A;  3WH0 A;  3ODK A;  2BA1 A;  2JX8 A;  4U84 A;  2YSI A;  2XP6 A;  2XP4 A;  2ZQU A;  2YAJ B;  2XP7 A;  2RE3 A;  3LE4 A;  3FS8 A;  5E66 A;  3KAF A;  2E45 A;  2ZR4 A;  2WAD A;  5AHT A;  3MQG A;  3OOB A;  3TC5 A;  2DMV A;  1K9R A;  3M7N A;  2MDI A;  2Y8N B;  2XPB A;  3LKX B;  3FSC A;  3M85 A;  5E64 A;  1YW5 A;  3FSB A;  3MCB A;  2QRV A;  5E5W A;  1I5H W;  1FLC A;  2ZAJ A;  4A0T A;  2YSH A;  1JMQ A;  2DK7 A;  3TDB A;  1WMV A;  2ZQT A;  2YSG A;  3KAB A;  3KAH A;  1EG3 A;  1RP5 A;  3PQH A;  3KAD A;  3NTP A;  2XPA A;  3MCB B;  2JMF A;  2L4J A;  2Q5A A;  2M8J A;  4E5R A;  4U85 A;  2OWO A;  2YSF A;  3CNG A;  5E65 A;  2JXW A;  3L4H A;  2ITK A;  4A0U A;  2DWV A;  2YSB A;  2XP9 A;  3MQH A;  4GLX A;  1F8A B;  2F21 A;  2ZR5 A;  2DK1 A;  3KAG A;  2XP5 A;  1NMV A;  5U47 A;  2LAJ A;  1K9Q A;  4U86 A;  2JV4 A;  4REX A;  2WAE A;  4QIB A;  1O6W A; 
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similar chains in the pdb database (?% sequence similarity)

 
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