2YAJB

Crystal structure of glycyl radical enzyme with bound substrate
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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publication title Structural Basis for a Kolbe-Type Decarboxylation Catalyzed by a Glycyl Radical Enzyme.
pubmed doi rcsb
molecule tags Lyase
source organism Clostridium scatologenes
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 2011-02-23

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; 2yajB01
2.20.70.100 Mainly Beta Single Sheet Ubiquitin Ligase Nedd4; Chain: W; Ubiquitin Ligase Nedd4; Chain: W; 2yajB02
2YAJB 2Y8NB
chains in the Genus database with same CATH superfamily
2XP3A 1NMVA 1O6WA 1WR7A 3PQHA 5E65A 2Q5AA 2XP5A 3MQHA 3FSCA 1ZCNA 2ZQSA 3MCBA 2ZR4A 3TC5A 3KAGA 2KXQA 4GLXA 2DJYA 1EG4A 3TDBA 2ZQUA 4REXA 2LAJA 2DK7A 2DK1A 2JX8A 3M7NA 2XP4A 1I5HW 1YW5A 3FS8A 1TK7A 2L4JA 2XP6A 1EG3A 2WADA 2JXWA 5E66A 4U85A 2RE3A 2F21A 1RP5A 2Y8NB 3KABA 3KAFA 3FSBA 5AHTA 4A0TA 2XP9A 3KAHA 3KADA 2WAEA 2OWOA 3WH0A 4QIBA 1K9QA 2BA1A 3LKXA 2E45A 2ZQTA 2ITKA 2ZR6A 2YSHA 2ZR5A 2DMVA 2MDIA 3MCBB 1JMQA 2M8JA 3OOBA 2XP8A 2XP7A 2YAJB 2EZ5W 4E5RA 5U47A 2ZAJA 3CNGA 3KAIA 2M3OW 4U84A 5E64A 3TCZA 2XPBA 3ODKA 3LKXB 5CQ2A 1K9RA 2JV4A 2YSBA 2YSGA 3M85A 2DWVA 1FLCA 2YSIA 3L4HA 3KCEA 1WMVA 1F8AB 1PINA 1TR8A 2M8IA 2XPAA 3NTPA 3LE4A 5E62A 5E5WA 2QRVA 4A0UA 2JMFA 4U86A 2ZQVA 3MQGA 2YSFA
chains in the Genus database with same CATH topology
2XP3A 1NMVA 1O6WA 1WR7A 3PQHA 5E65A 2Q5AA 2XP5A 3MQHA 3FSCA 1ZCNA 2ZQSA 3MCBA 2ZR4A 3TC5A 3KAGA 2KXQA 4GLXA 2DJYA 1EG4A 3TDBA 2ZQUA 4REXA 2LAJA 2DK7A 2DK1A 2JX8A 3M7NA 2XP4A 1I5HW 1YW5A 3FS8A 1TK7A 2L4JA 2XP6A 1EG3A 2WADA 2JXWA 5E66A 4U85A 2RE3A 2F21A 1RP5A 2Y8NB 3KABA 3KAFA 3FSBA 5AHTA 4A0TA 2XP9A 3KAHA 3KADA 2WAEA 2OWOA 3WH0A 4QIBA 1K9QA 2BA1A 3LKXA 2E45A 2ZQTA 2ITKA 2ZR6A 2YSHA 2ZR5A 2DMVA 2MDIA 3MCBB 1JMQA 2M8JA 3OOBA 2XP8A 2XP7A 2YAJB 2EZ5W 4E5RA 5U47A 2ZAJA 3CNGA 3KAIA 2M3OW 4U84A 5E64A 3TCZA 2XPBA 3ODKA 3LKXB 5CQ2A 1K9RA 2JV4A 2YSBA 2YSGA 3M85A 2DWVA 1FLCA 2YSIA 3L4HA 3KCEA 1WMVA 1F8AB 1PINA 1TR8A 2M8IA 2XPAA 3NTPA 3LE4A 5E62A 5E5WA 2QRVA 4A0UA 2JMFA 4U86A 2ZQVA 3MQGA 2YSFA
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
 2XP3 A;  1NMV A;  1O6W A;  1WR7 A;  3PQH A;  5E65 A;  2Q5A A;  2XP5 A;  3MQH A;  3FSC A;  1ZCN A;  2ZQS A;  3MCB A;  2ZR4 A;  3TC5 A;  3KAG A;  2KXQ A;  4GLX A;  2DJY A;  1EG4 A;  3TDB A;  2ZQU A;  4REX A;  2LAJ A;  2DK7 A;  2DK1 A;  2JX8 A;  3M7N A;  2XP4 A;  1I5H W;  1YW5 A;  3FS8 A;  1TK7 A;  2L4J A;  2XP6 A;  1EG3 A;  2WAD A;  2JXW A;  5E66 A;  4U85 A;  2RE3 A;  2F21 A;  1RP5 A;  2Y8N B;  3KAB A;  3KAF A;  3FSB A;  5AHT A;  4A0T A;  2XP9 A;  3KAH A;  3KAD A;  2WAE A;  2OWO A;  3WH0 A;  4QIB A;  1K9Q A;  2BA1 A;  3LKX A;  2E45 A;  2ZQT A;  2ITK A;  2ZR6 A;  2YSH A;  2ZR5 A;  2DMV A;  2MDI A;  3MCB B;  1JMQ A;  2M8J A;  3OOB A;  2XP8 A;  2XP7 A;  2YAJ B;  2EZ5 W;  4E5R A;  5U47 A;  2ZAJ A;  3CNG A;  3KAI A;  2M3O W;  4U84 A;  5E64 A;  3TCZ A;  2XPB A;  3ODK A;  3LKX B;  5CQ2 A;  1K9R A;  2JV4 A;  2YSB A;  2YSG A;  3M85 A;  2DWV A;  1FLC A;  2YSI A;  3L4H A;  3KCE A;  1WMV A;  1F8A B;  1PIN A;  1TR8 A;  2M8I A;  2XPA A;  3NTP A;  3LE4 A;  5E62 A;  5E5W A;  2QRV A;  4A0U A;  2JMF A;  4U86 A;  2ZQV A;  3MQG A;  2YSF A; 
#chains in the Genus database with same CATH homology
 2XP3 A;  1NMV A;  1O6W A;  1WR7 A;  3PQH A;  5E65 A;  2Q5A A;  2XP5 A;  3MQH A;  3FSC A;  1ZCN A;  2ZQS A;  3MCB A;  2ZR4 A;  3TC5 A;  3KAG A;  2KXQ A;  4GLX A;  2DJY A;  1EG4 A;  3TDB A;  2ZQU A;  4REX A;  2LAJ A;  2DK7 A;  2DK1 A;  2JX8 A;  3M7N A;  2XP4 A;  1I5H W;  1YW5 A;  3FS8 A;  1TK7 A;  2L4J A;  2XP6 A;  1EG3 A;  2WAD A;  2JXW A;  5E66 A;  4U85 A;  2RE3 A;  2F21 A;  1RP5 A;  2Y8N B;  3KAB A;  3KAF A;  3FSB A;  5AHT A;  4A0T A;  2XP9 A;  3KAH A;  3KAD A;  2WAE A;  2OWO A;  3WH0 A;  4QIB A;  1K9Q A;  2BA1 A;  3LKX A;  2E45 A;  2ZQT A;  2ITK A;  2ZR6 A;  2YSH A;  2ZR5 A;  2DMV A;  2MDI A;  3MCB B;  1JMQ A;  2M8J A;  3OOB A;  2XP8 A;  2XP7 A;  2YAJ B;  2EZ5 W;  4E5R A;  5U47 A;  2ZAJ A;  3CNG A;  3KAI A;  2M3O W;  4U84 A;  5E64 A;  3TCZ A;  2XPB A;  3ODK A;  3LKX B;  5CQ2 A;  1K9R A;  2JV4 A;  2YSB A;  2YSG A;  3M85 A;  2DWV A;  1FLC A;  2YSI A;  3L4H A;  3KCE A;  1WMV A;  1F8A B;  1PIN A;  1TR8 A;  2M8I A;  2XPA A;  3NTP A;  3LE4 A;  5E62 A;  5E5W A;  2QRV A;  4A0U A;  2JMF A;  4U86 A;  2ZQV A;  3MQG A;  2YSF A; 
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similar chains in the pdb database (?% sequence similarity)

 
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