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


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