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