1F6UA

Nmr structure of the hiv-1 nucleocapsid protein bound to stem-loop sl2 of the psi-rna packaging signal. implications for genome recognition
Total Genus 9
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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
9
sequence length
55
structure length
55
Chain Sequence
MQKGNFRNQRKTVKCFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDCTERQAN
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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 tags Structural protein/rna
molecule keywords HIV-1 STEM-LOOP SL2 FROM PSI-RNA PACKAGING
publication title NMR structure of the HIV-1 nucleocapsid protein bound to stem-loop SL2 of the psi-RNA packaging signal. Implications for genome recognition.
pubmed doi rcsb
source organism Human immunodeficiency virus 1
total genus 9
structure length 55
sequence length 55
ec nomenclature ec 2.7.7.49: RNA-directed DNA polymerase.
pdb deposition date 2000-06-23

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF00098 zf-CCHC Zinc knuckle
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
4.10.60.10 Few Secondary Structures Irregular HIV-1 Nucleocapsid Protein Zinc finger, CCHC-type 1f6uA00
1Q3ZA 1AAFA 2EC7A 3TS0A 3TRZA 2YSAA 1WWEA 1A1TA 1A6BB 2L4LA 2M3ZA 2JZWA 1MFSA 1U6PA 2IHXA 3TS2A 2CQFA 1WWDA 1WWFA 3NYBB 1WWGA 1ESKA 2EXFA 1Q3YA 2LI8A 1F6UA 1BJ6A
chains in the Genus database with same CATH superfamily
1Q3ZA 1AAFA 2EC7A 3TS0A 3TRZA 2YSAA 1WWEA 1A1TA 1A6BB 2L4LA 2M3ZA 2JZWA 1MFSA 1U6PA 2IHXA 3TS2A 2CQFA 1WWDA 1WWFA 3NYBB 1WWGA 1ESKA 2EXFA 1Q3YA 2LI8A 1F6UA 1BJ6A
chains in the Genus database with same CATH topology
1Q3ZA 1AAFA 2EC7A 3TS0A 3TRZA 2YSAA 1WWEA 1A1TA 1A6BB 2L4LA 2M3ZA 2JZWA 1MFSA 1U6PA 2IHXA 3TS2A 2CQFA 1WWDA 1WWFA 3NYBB 1WWGA 1ESKA 2EXFA 1Q3YA 2LI8A 1F6UA 1BJ6A
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 1Q3Z A;  1AAF A;  2EC7 A;  3TS0 A;  3TRZ A;  2YSA A;  1WWE A;  1A1T A;  1A6B B;  2L4L A;  2M3Z A;  2JZW A;  1MFS A;  1U6P A;  2IHX A;  3TS2 A;  2CQF A;  1WWD A;  1WWF A;  3NYB B;  1WWG A;  1ESK A;  2EXF A;  1Q3Y A;  2LI8 A;  1F6U A;  1BJ6 A; 
#chains in the Genus database with same CATH topology
 1Q3Z A;  1AAF A;  2EC7 A;  3TS0 A;  3TRZ A;  2YSA A;  1WWE A;  1A1T A;  1A6B B;  2L4L A;  2M3Z A;  2JZW A;  1MFS A;  1U6P A;  2IHX A;  3TS2 A;  2CQF A;  1WWD A;  1WWF A;  3NYB B;  1WWG A;  1ESK A;  2EXF A;  1Q3Y A;  2LI8 A;  1F6U A;  1BJ6 A; 
#chains in the Genus database with same CATH homology
 1Q3Z A;  1AAF A;  2EC7 A;  3TS0 A;  3TRZ A;  2YSA A;  1WWE A;  1A1T A;  1A6B B;  2L4L A;  2M3Z A;  2JZW A;  1MFS A;  1U6P A;  2IHX A;  3TS2 A;  2CQF A;  1WWD A;  1WWF A;  3NYB B;  1WWG A;  1ESK A;  2EXF A;  1Q3Y A;  2LI8 A;  1F6U A;  1BJ6 A; 
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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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