3JD74

The novel asymmetric entry intermediate of a picornavirus captured with nanodiscs
Total Genus 3
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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
3
sequence length
68
structure length
56
Chain Sequence
GAQVSTQKTGAIHYTNINYYKDAASNSANRQDFTQDPSKFTEPVKDIMIKSLPALN
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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 Capsid protein VP1
publication title The novel asymmetric entry intermediate of a picornavirus captured with nanodiscs.
pubmed doi rcsb
molecule tags Virus
total genus 3
structure length 56
sequence length 68
ec nomenclature
pdb deposition date 2016-04-29

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
4 PF02226 Pico_P1A Picornavirus coat protein (VP4)
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
4.10.80.10 Few Secondary Structures Irregular Rhinovirus 14, subunit 4 Picornavirus coat protein VP4 3jd7400
1AR84 1NCQD 1AR64 1NA1D 1PO14 1RUF4 4Q4V4 1RHI4 2PLV4 1HRV4 1RUJ4 4Q4Y4 1VBB4 4PDWD 1HRI4 4GB34 1AL24 2HWC4 1AR74 1RUD4 1RUH4 2R064 2RS34 1PIV4 1POV0 1RUC4 1HXS4 2RS14 2R044 1VBE4 1RVF4 1PO24 1BEV4 1VBC4 2RMU4 2RR14 1MQTD 2RS54 1RMU4 2RM24 4RHV4 1EAH4 3JBG4 2R074 1RUI4 1D4M4 1RUE4 4Q4W4 1Z7S4 2X5ID 4Q4X4 1EV14 1COV4 1PVC4 1R094 1R084 1RUG4 1H8TD 1OOPD 2HWB4 3JD74 3J8F4 1VBD4 1VBA4 1ASJ4 1K5MD 1AR94 1VRH4
chains in the Genus database with same CATH superfamily
1AR84 1NCQD 1AR64 4Q4V4 4KX6A 4Q4Y4 4YTMA 1RUD4 2RS34 1HXS4 1BEV4 3VR9A 1RMU4 3VRAA 1D4M4 1RUE4 3P4SA 4Q4W4 4Q4X4 2WS3A 1EV14 1COV4 1PVC4 3AEDA 3GQHA 3P4QA 3AE8A 4YSXA 1NEKA 3AECA 2R7FA 1H8TD 3JD74 1RUF4 1NA1D 3SFEA 4YTNA 1RHI4 1HRV4 2PYJA 1VBB4 3AE7A 1HRI4 4GB34 3AE3A 3P4RA 1AL24 2HWC4 3AEGA 3AE4A 2RS14 1VBE4 1RVF4 1VBC4 3SFDA 3VR8A 1MQTD 2RM24 2PYLA 1EAH4 3JBG4 1KF6A 1RUI4 2WDRA 5C2TA 1XHZA 3AEAA 1R084 2HWB4 3ABVA 3AEBA 1VBD4 1VBA4 1RUG4 3AE2A 2PLV4 1RUJ4 4YT0A 2R064 1L0VA 1YQ3A 2PZSA 1PIV4 1RUC4 1YQ4A 2H89A 4YTPA 2RS54 4RHV4 3GQKA 3AEFA 3P4PA 2WU5A 2R074 3FI7A 2X5ID 3VRBA 1XI1A 2PW9A 2PY5A 2WP9A 2WDQA 1XHXA 4YSYA 1ASJ4 1AR94 1PO14 1NENA 4YSZA 3CIRA 2H88A 4YXDA 1AR74 2WU2A 1POV0 2FBWA 2WQYA 2WDVA 3AE1A 2R044 4PDWD 3AE5A 1PO24 2RMU4 1ZP0A 2RR14 3AEEA 5C3JA 2EX3A 2B76A 3AE6A 1Z7S4 3SUCA 3AE9A 2ACZA 1R094 1ZOYA 1KFYA 1OOPD 3J8F4 1RUH4 1K5MD 1VRH4
chains in the Genus database with same CATH topology
1AR84 1NCQD 1AR64 1NA1D 1PO14 1RUF4 4Q4V4 1RHI4 2PLV4 1HRV4 1RUJ4 4Q4Y4 1VBB4 4PDWD 1HRI4 4GB34 1AL24 2HWC4 1AR74 1RUD4 1RUH4 2R064 2RS34 1PIV4 1POV0 1RUC4 1HXS4 2RS14 2R044 1VBE4 1RVF4 1PO24 1BEV4 1VBC4 2RMU4 2RR14 1MQTD 2RS54 1RMU4 2RM24 4RHV4 1EAH4 3JBG4 2R074 1RUI4 1D4M4 1RUE4 4Q4W4 1Z7S4 2X5ID 4Q4X4 1EV14 1COV4 1PVC4 1R094 1R084 1RUG4 1H8TD 1OOPD 2HWB4 3JD74 3J8F4 1VBD4 1VBA4 1ASJ4 1K5MD 1AR94 1VRH4
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 1AR8 4;  1NCQ D;  1AR6 4;  1NA1 D;  1PO1 4;  1RUF 4;  4Q4V 4;  1RHI 4;  2PLV 4;  1HRV 4;  1RUJ 4;  4Q4Y 4;  1VBB 4;  4PDW D;  1HRI 4;  4GB3 4;  1AL2 4;  2HWC 4;  1AR7 4;  1RUD 4;  1RUH 4;  2R06 4;  2RS3 4;  1PIV 4;  1POV 0;  1RUC 4;  1HXS 4;  2RS1 4;  2R04 4;  1VBE 4;  1RVF 4;  1PO2 4;  1BEV 4;  1VBC 4;  2RMU 4;  2RR1 4;  1MQT D;  2RS5 4;  1RMU 4;  2RM2 4;  4RHV 4;  1EAH 4;  3JBG 4;  2R07 4;  1RUI 4;  1D4M 4;  1RUE 4;  4Q4W 4;  1Z7S 4;  2X5I D;  4Q4X 4;  1EV1 4;  1COV 4;  1PVC 4;  1R09 4;  1R08 4;  1RUG 4;  1H8T D;  1OOP D;  2HWB 4;  3JD7 4;  3J8F 4;  1VBD 4;  1VBA 4;  1ASJ 4;  1K5M D;  1AR9 4;  1VRH 4; 
#chains in the Genus database with same CATH topology
 1AR8 4;  1NCQ D;  1AR6 4;  4Q4V 4;  4KX6 A;  4Q4Y 4;  4YTM A;  1RUD 4;  2RS3 4;  1HXS 4;  1BEV 4;  3VR9 A;  1RMU 4;  3VRA A;  1D4M 4;  1RUE 4;  3P4S A;  4Q4W 4;  4Q4X 4;  2WS3 A;  1EV1 4;  1COV 4;  1PVC 4;  3AED A;  3GQH A;  3P4Q A;  3AE8 A;  4YSX A;  1NEK A;  3AEC A;  2R7F A;  1H8T D;  3JD7 4;  1RUF 4;  1NA1 D;  3SFE A;  4YTN A;  1RHI 4;  1HRV 4;  2PYJ A;  1VBB 4;  3AE7 A;  1HRI 4;  4GB3 4;  3AE3 A;  3P4R A;  1AL2 4;  2HWC 4;  3AEG A;  3AE4 A;  2RS1 4;  1VBE 4;  1RVF 4;  1VBC 4;  3SFD A;  3VR8 A;  1MQT D;  2RM2 4;  2PYL A;  1EAH 4;  3JBG 4;  1KF6 A;  1RUI 4;  2WDR A;  5C2T A;  1XHZ A;  3AEA A;  1R08 4;  2HWB 4;  3ABV A;  3AEB A;  1VBD 4;  1VBA 4;  1RUG 4;  3AE2 A;  2PLV 4;  1RUJ 4;  4YT0 A;  2R06 4;  1L0V A;  1YQ3 A;  2PZS A;  1PIV 4;  1RUC 4;  1YQ4 A;  2H89 A;  4YTP A;  2RS5 4;  4RHV 4;  3GQK A;  3AEF A;  3P4P A;  2WU5 A;  2R07 4;  3FI7 A;  2X5I D;  3VRB A;  1XI1 A;  2PW9 A;  2PY5 A;  2WP9 A;  2WDQ A;  1XHX A;  4YSY A;  1ASJ 4;  1AR9 4;  1PO1 4;  1NEN A;  4YSZ A;  3CIR A;  2H88 A;  4YXD A;  1AR7 4;  2WU2 A;  1POV 0;  2FBW A;  2WQY A;  2WDV A;  3AE1 A;  2R04 4;  4PDW D;  3AE5 A;  1PO2 4;  2RMU 4;  1ZP0 A;  2RR1 4;  3AEE A;  5C3J A;  2EX3 A;  2B76 A;  3AE6 A;  1Z7S 4;  3SUC A;  3AE9 A;  2ACZ A;  1R09 4;  1ZOY A;  1KFY A;  1OOP D;  3J8F 4;  1RUH 4;  1K5M D;  1VRH 4; 
#chains in the Genus database with same CATH homology
 1AR8 4;  1NCQ D;  1AR6 4;  1NA1 D;  1PO1 4;  1RUF 4;  4Q4V 4;  1RHI 4;  2PLV 4;  1HRV 4;  1RUJ 4;  4Q4Y 4;  1VBB 4;  4PDW D;  1HRI 4;  4GB3 4;  1AL2 4;  2HWC 4;  1AR7 4;  1RUD 4;  1RUH 4;  2R06 4;  2RS3 4;  1PIV 4;  1POV 0;  1RUC 4;  1HXS 4;  2RS1 4;  2R04 4;  1VBE 4;  1RVF 4;  1PO2 4;  1BEV 4;  1VBC 4;  2RMU 4;  2RR1 4;  1MQT D;  2RS5 4;  1RMU 4;  2RM2 4;  4RHV 4;  1EAH 4;  3JBG 4;  2R07 4;  1RUI 4;  1D4M 4;  1RUE 4;  4Q4W 4;  1Z7S 4;  2X5I D;  4Q4X 4;  1EV1 4;  1COV 4;  1PVC 4;  1R09 4;  1R08 4;  1RUG 4;  1H8T D;  1OOP D;  2HWB 4;  3JD7 4;  3J8F 4;  1VBD 4;  1VBA 4;  1ASJ 4;  1K5M D;  1AR9 4;  1VRH 4; 
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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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