1K5MD

Crystal structure of a human rhinovirus type 14:human immunodeficiency virus type 1 v3 loop chimeric virus mn-iii-2
Total Genus 2

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

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
source organism Human rhinovirus 14
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
molecule keywords COAT PROTEIN VP1 (P1D)
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
4Q4X4 1PO24 1VBC4 2RS34 1PIV4 1RUF4 1RUJ4 4Q4W4 2RM24 1ASJ4 1Z7S4 1BEV4 2HWB4 4Q4V4 1OOPD 1RHI4 1R084 1AR74 1H8TD 2HWC4 3JBG4 3JD74 4GB34 1HXS4 1AR64 1EAH4 1POV0 1R094 1EV14 1RUE4 2PLV4 4RHV4 1PO14 4PDWD 1NCQD 1D4M4 1RUD4 1RUC4 1RVF4 1COV4 2R074 2RR14 1PVC4 2RS14 1RUI4 1NA1D 1MQTD 1RUG4 1VBD4 1AL24 1VRH4 4Q4Y4 2R064 1K5MD 1AR94 1VBA4 1AR84 1VBB4 1HRI4 2X5ID 1HRV4 2R044 2RMU4 1RMU4 1RUH4 1VBE4 2RS54 3J8F4
chains in the Genus database with same CATH superfamily
3P4QA 2RM24 3AEBA 4YTNA 1RHI4 2WQYA 3JD74 4GB34 4KX6A 2PLV4 1EV14 2WDQA 2WDRA 2ACZA 3VRAA 3CIRA 1RUD4 2H88A 4YXDA 2R074 1KF6A 2RR14 2WU5A 1XHZA 3SUCA 3AE9A 3P4PA 2PW9A 3AEGA 1HRV4 3FI7A 3GQKA 3AE4A 4Q4X4 3GQHA 2RS34 3AE5A 3VRBA 4Q4V4 2EX3A 2PY5A 1R084 1AR74 1HXS4 3AEAA 4RHV4 1NEKA 3VR8A 1PO14 2WS3A 3VR9A 3AEFA 4YT0A 1NCQD 3AE3A 1L0VA 1RUC4 1XHXA 2PYLA 1RUI4 1MQTD 1AL24 4Q4Y4 2R064 3AE7A 3AE6A 1AR84 3P4RA 2R044 1RMU4 1RUH4 3J8F4 1PO24 2R7FA 1PIV4 1RUF4 1Z7S4 1BEV4 2HWB4 2B76A 1YQ4A 2HWC4 3ABVA 3JBG4 1POV0 1EAH4 1RUE4 3P4SA 1D4M4 2PYJA 5C3JA 2FBWA 2WDVA 1PVC4 1NA1D 1RUG4 3AE2A 1NENA 1K5MD 1AR94 1VBA4 1VBB4 2X5ID 3AEEA 3SFEA 4YTPA 3SFDA 2WP9A 1VBE4 1VBC4 4Q4W4 1RUJ4 1ASJ4 3AECA 4YSYA 1ZOYA 1KFYA 1OOPD 1YQ3A 1H8TD 1ZP0A 1AR64 1R094 3AEDA 4PDWD 4YSZA 5C2TA 3AE1A 1RVF4 1COV4 2H89A 4YTMA 2RS14 1VBD4 1VRH4 3AE8A 2PZSA 1HRI4 4YSXA 1XI1A 2RMU4 2WU2A 2RS54
chains in the Genus database with same CATH topology
4Q4X4 1PO24 1VBC4 2RS34 1PIV4 1RUF4 1RUJ4 4Q4W4 2RM24 1ASJ4 1Z7S4 1BEV4 2HWB4 4Q4V4 1OOPD 1RHI4 1R084 1AR74 1H8TD 2HWC4 3JBG4 3JD74 4GB34 1HXS4 1AR64 1EAH4 1POV0 1R094 1EV14 1RUE4 2PLV4 4RHV4 1PO14 4PDWD 1NCQD 1D4M4 1RUD4 1RUC4 1RVF4 1COV4 2R074 2RR14 1PVC4 2RS14 1RUI4 1NA1D 1MQTD 1RUG4 1VBD4 1AL24 1VRH4 4Q4Y4 2R064 1K5MD 1AR94 1VBA4 1AR84 1VBB4 1HRI4 2X5ID 1HRV4 2R044 2RMU4 1RMU4 1RUH4 1VBE4 2RS54 3J8F4
chains in the Genus database with same CATH homology


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