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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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 2011-02-23

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