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
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
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
2YAJB 2Y8NB
chains in the Genus database with same CATH superfamily
2YAJB 1K9QA 2E45A 2XP7A 2XPBA 2YSGA 1RP5A 1TR8A 2JMFA 1NMVA 2YSIA 2RE3A 3NTPA 2YSHA 1TK7A 2YSBA 2XP3A 2DJYA 3MCBB 2DK1A 4U86A 3KADA 2M8JA 2XP9A 3KCEA 2DK7A 2YSFA 2BA1A 2QRVA 3FSBA 2KXQA 3LE4A 3KABA 5E62A 1EG4A 2ZR5A 2ITKA 2M8IA 5CQ2A 2ZQUA 3KAIA 3FS8A 2JX8A 1I5HW 3TDBA 1K9RA 3KAGA 1PINA 3WH0A 5U47A 3PQHA 2XP6A 1F8AB 2MDIA 2WADA 3ODKA 5E5WA 3TCZA 2XP4A 2XP8A 3LKXA 1EG3A 3M7NA 2ZAJA 4QIBA 1WMVA 3L4HA 3TC5A 5E64A 2LAJA 2XP5A 3KAHA 2ZQSA 3M85A 4A0TA 2Q5AA 5E66A 3OOBA 2JXWA 1WR7A 2EZ5W 5AHTA 2L4JA 2ZR6A 1YW5A 4A0UA 3LKXB 1FLCA 3CNGA 1ZCNA 2ZR4A 4U84A 1JMQA 4GLXA 3MQHA 2ZQVA 2Y8NB 4REXA 2M3OW 3KAFA 2JV4A 2DMVA 4E5RA 2OWOA 2F21A 3MCBA 3FSCA 2ZQTA 3MQGA 2WAEA 2XPAA 2DWVA 4U85A 5E65A 1O6WA
chains in the Genus database with same CATH topology
2YAJB 1K9QA 2E45A 2XP7A 2XPBA 2YSGA 1RP5A 1TR8A 2JMFA 1NMVA 2YSIA 2RE3A 3NTPA 2YSHA 1TK7A 2YSBA 2XP3A 2DJYA 3MCBB 2DK1A 4U86A 3KADA 2M8JA 2XP9A 3KCEA 2DK7A 2YSFA 2BA1A 2QRVA 3FSBA 2KXQA 3LE4A 3KABA 5E62A 1EG4A 2ZR5A 2ITKA 2M8IA 5CQ2A 2ZQUA 3KAIA 3FS8A 2JX8A 1I5HW 3TDBA 1K9RA 3KAGA 1PINA 3WH0A 5U47A 3PQHA 2XP6A 1F8AB 2MDIA 2WADA 3ODKA 5E5WA 3TCZA 2XP4A 2XP8A 3LKXA 1EG3A 3M7NA 2ZAJA 4QIBA 1WMVA 3L4HA 3TC5A 5E64A 2LAJA 2XP5A 3KAHA 2ZQSA 3M85A 4A0TA 2Q5AA 5E66A 3OOBA 2JXWA 1WR7A 2EZ5W 5AHTA 2L4JA 2ZR6A 1YW5A 4A0UA 3LKXB 1FLCA 3CNGA 1ZCNA 2ZR4A 4U84A 1JMQA 4GLXA 3MQHA 2ZQVA 2Y8NB 4REXA 2M3OW 3KAFA 2JV4A 2DMVA 4E5RA 2OWOA 2F21A 3MCBA 3FSCA 2ZQTA 3MQGA 2WAEA 2XPAA 2DWVA 4U85A 5E65A 1O6WA
chains in the Genus database with same CATH homology


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