3JD7 | Genus

Total Genus 3

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

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

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After clicking on a point (x,y) in the genus matrix above, a subchain from x to y is shown in color.

Genus data interpretation

Chord Diagram

molecule tags	Virus
publication title	The novel asymmetric entry intermediate of a picornavirus captured with nanodiscs. pubmed doi rcsb
molecule keywords	Capsid protein VP1
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	Class	Architecture	Topology	Homology	Domain
4.10.80.10	Few Secondary Structures	Irregular	Rhinovirus 14, subunit 4	Picornavirus coat protein VP4	3jd7400

1PO24 1NCQD 4Q4X4 2R074 1H8TD 2RS14 1BEV4 2R044 1AR94 2PLV4 1RUH4 4Q4V4 2RR14 1AR74 4Q4Y4 1R084 1AL24 1ASJ4 1RUD4 1OOPD 2HWC4 1HRI4 2RMU4 1RVF4 1AR64 1D4M4 1RUJ4 1RHI4 1VRH4 1PIV4 3JBG4 1RMU4 1Z7S4 1VBA4 1VBE4 1VBB4 1K5MD 1EAH4 4PDWD 1MQTD 1VBC4 1COV4 1POV0 2HWB4 2RS34 1EV14 1R094 1PVC4 1RUC4 4Q4W4 2X5ID 1HRV4 2R064 4GB34 1PO14 3J8F4 1RUF4 3JD74 2RS54 1RUI4 1NA1D 1RUG4 1AR84 1RUE4 4RHV4 1VBD4 1HXS4 2RM24
chains in the Genus database with same CATH superfamily

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

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

#similar chains in the Genus database (?% sequence similarity)
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#similar chains, but unknotted
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#similar chains in the pdb database (?% sequence similarity)
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3JD74

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations