1K5MD

Crystal structure of a human rhinovirus type 14:human immunodeficiency virus type 1 v3 loop chimeric virus mn-iii-2
Total Genus 2
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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
2
sequence length
40
structure length
40
Chain Sequence
INYYKDAASTSSAGQSLSMDPSKFTEPVKDLMLKGAPALN
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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.

molecule tags Virus
molecule keywords COAT PROTEIN VP1 (P1D)
publication title Crystal Structure of a Human Rhinovirus that Displays Part of the HIV-1 V3 Loop and Induces Neutralizing Antibodies against HIV-1
pubmed doi rcsb
source organism Human rhinovirus 14
total genus 2
structure length 40
sequence length 40
ec nomenclature ec 2.7.7.48: RNA-directed RNA polymerase.
pdb deposition date 2001-10-11

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
D 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 1k5mD00
1AL24 2PLV4 1K5MD 1R084 1Z7S4 4Q4X4 1EV14 1RUD4 1RUE4 1VRH4 2HWC4 2RS54 2X5ID 4RHV4 1VBE4 2R044 1PVC4 3J8F4 1D4M4 2R074 1PIV4 1H8TD 1HRI4 1MQTD 1NCQD 1OOPD 2RM24 2RMU4 1RMU4 1RUJ4 1R094 1RUH4 1HRV4 2RS14 1POV0 2RS34 1AR84 1AR94 1HXS4 1RVF4 1EAH4 1NA1D 4GB34 1RUI4 3JBG4 1ASJ4 1RUG4 1VBA4 1VBD4 1AR74 4Q4Y4 1PO24 1RUF4 2R064 1VBC4 3JD74 4Q4V4 4PDWD 1PO14 1VBB4 2HWB4 1AR64 4Q4W4 1BEV4 2RR14 1RUC4 1COV4 1RHI4
chains in the Genus database with same CATH superfamily
3CIRA 1R084 2WU2A 1XHXA 1ZP0A 1VRH4 3AECA 2X5ID 1YQ4A 2R7FA 3VRAA 3AE1A 1PVC4 3SUCA 1PIV4 1OOPD 2PYJA 2RMU4 4YSYA 3AE5A 5C3JA 2RS14 4GB34 1EAH4 1NA1D 1ZOYA 3AEGA 1PO24 3SFDA 1NENA 5C2TA 4Q4W4 2WS3A 1BEV4 1XHZA 1RHI4 1Z7S4 3VRBA 1VBE4 3J8F4 1D4M4 1H8TD 3FI7A 1MQTD 1RMU4 3GQKA 1XI1A 1RUH4 4YTPA 1RVF4 2PYLA 2WU5A 1ASJ4 1VBD4 3ABVA 3SFEA 1RUF4 1VBC4 3JD74 4Q4V4 2WDRA 4YT0A 4PDWD 3VR9A 3P4RA 1YQ3A 2HWB4 1AR64 3AE4A 3AE9A 4KX6A 1RUC4 1NEKA 1K5MD 3GQHA 2WQYA 4Q4X4 1RUD4 3AE2A 3AEEA 1KFYA 2PW9A 2RS54 2WDQA 4YTNA 1KF6A 1RUJ4 1R094 2EX3A 2WDVA 3AE6A 1AR84 1AR94 1HXS4 2PZSA 1RUI4 3P4PA 4Q4Y4 4YSZA 1AR74 2B76A 2H88A 4YXDA 4YSXA 2RR14 1AL24 4YTMA 2PLV4 2PY5A 1EV14 1L0VA 1RUE4 2HWC4 4RHV4 2R044 3AEBA 2R074 1HRI4 1NCQD 2RM24 3AEFA 3P4QA 3AE8A 1HRV4 1POV0 3AE7A 3VR8A 2WP9A 3JBG4 1RUG4 1VBA4 2R064 3AE3A 1COV4 3AEDA 2ACZA 3P4SA 1PO14 1VBB4 3AEAA 2FBWA 2H89A 2RS34
chains in the Genus database with same CATH topology
1AL24 2PLV4 1K5MD 1R084 1Z7S4 4Q4X4 1EV14 1RUD4 1RUE4 1VRH4 2HWC4 2RS54 2X5ID 4RHV4 1VBE4 2R044 1PVC4 3J8F4 1D4M4 2R074 1PIV4 1H8TD 1HRI4 1MQTD 1NCQD 1OOPD 2RM24 2RMU4 1RMU4 1RUJ4 1R094 1RUH4 1HRV4 2RS14 1POV0 2RS34 1AR84 1AR94 1HXS4 1RVF4 1EAH4 1NA1D 4GB34 1RUI4 3JBG4 1ASJ4 1RUG4 1VBA4 1VBD4 1AR74 4Q4Y4 1PO24 1RUF4 2R064 1VBC4 3JD74 4Q4V4 4PDWD 1PO14 1VBB4 2HWB4 1AR64 4Q4W4 1BEV4 2RR14 1RUC4 1COV4 1RHI4
chains in the Genus database with same CATH homology


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