2YAJB

Crystal structure of glycyl radical enzyme with bound substrate
Total Genus 18
Loading diagram...

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
Loading diagram...

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
{{ tooltip.sname }} connected with {{ tooltip.tname }} : {{qFormat(tooltip.svalue) }}
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 2011-02-23

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

 
#similar chains in the Genus database (?% sequence similarity)
...loading similar chains, please wait...
#similar chains, but unknotted
...loading similar chains, please wait...
#similar chains in the pdb database (?% sequence similarity)
...loading similar chains, please wait...