4NX4C

Re-refinement of cap-1 hiv-ca complex
Total Genus 47
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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
47
sequence length
145
structure length
145
Chain Sequence
b'PIVQNLQGQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKRWIILGLNKIVRMY'
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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 keywords Gag-Pol polyprotein
publication title Protein structural ensembles are revealed by redefining X-ray electron density noise.
pubmed doi rcsb
source organism Human immunodeficiency virus type 1
molecule tags Viral protein
total genus 47
structure length 145
sequence length 145
ec nomenclature ec 2.7.7.49: RNA-directed DNA polymerase.
pdb deposition date 2013-12-08
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
1.10.375.10 Mainly Alpha Orthogonal Bundle Human Immunodeficiency Virus Type 1 Capsid Protein Human Immunodeficiency Virus Type 1 Capsid Protein 4nx4C00
4U0DA 4PH3A 2PXRC 4HTWA 4WYMA 2GOLB 4XFYA 1E6JP 5HGOA 1M9XC 3BP9A 1U7KA 2LF4A 4PH0A 1G03A 4U0BA 3H4EA 4DGEC 4E91A 4E92A 4LQWC 2M8LA 1M9EC 2WLVA 4XRQA 5HGNA 2X2DD 3NTEA 5JPAA 1AFVA 5HGMA 2GONA 2X83A 4PH2A 4U0AA 2EIAA 2X82A 2XGUA 4NX4C 4U0FA 4DGAC 5HGLA 4XFZA 1M9DC 2XDEA 1EM9A 1EIAA 3H47A 1L6NA 4INBA 1GWPA 5HGKA 2XGVA 4QNBA 1D1DA 1AK4C 2V4XA 4J93A 4XROA 2PWMA 2XGYA 1M9CC 1M9FC 1P7NA 2Y4ZA 2M8NA 2PWOA 2JPRA 4U0CA 1QRJA 3P05A 2M8PA 2KGFA 3MGEA 4XFXA 4U0EA 4B4NA 1M9YC 2WLVB
chains in the Genus database with same CATH superfamily
4U0DA 4PH3A 2PXRC 4HTWA 4WYMA 2GOLB 4XFYA 1E6JP 5HGOA 1M9XC 3BP9A 1U7KA 2LF4A 4PH0A 1G03A 4U0BA 3H4EA 4DGEC 4E91A 4E92A 4LQWC 2M8LA 1M9EC 2WLVA 4XRQA 5HGNA 2X2DD 3NTEA 5JPAA 1AFVA 5HGMA 2GONA 2X83A 4PH2A 4U0AA 2EIAA 2X82A 2XGUA 4NX4C 4U0FA 4DGAC 5HGLA 4XFZA 1M9DC 2XDEA 1EM9A 1EIAA 3H47A 1L6NA 4INBA 1GWPA 5HGKA 2XGVA 4QNBA 1D1DA 1AK4C 2V4XA 4J93A 4XROA 2PWMA 2XGYA 1M9CC 1M9FC 1P7NA 2Y4ZA 2M8NA 2PWOA 2JPRA 4U0CA 1QRJA 3P05A 2M8PA 2KGFA 3MGEA 4XFXA 4U0EA 4B4NA 1M9YC 2WLVB
chains in the Genus database with same CATH topology
4U0DA 4PH3A 2PXRC 4HTWA 4WYMA 2GOLB 4XFYA 1E6JP 5HGOA 1M9XC 3BP9A 1U7KA 2LF4A 4PH0A 1G03A 4U0BA 3H4EA 4DGEC 4E91A 4E92A 4LQWC 2M8LA 1M9EC 2WLVA 4XRQA 5HGNA 2X2DD 3NTEA 5JPAA 1AFVA 5HGMA 2GONA 2X83A 4PH2A 4U0AA 2EIAA 2X82A 2XGUA 4NX4C 4U0FA 4DGAC 5HGLA 4XFZA 1M9DC 2XDEA 1EM9A 1EIAA 3H47A 1L6NA 4INBA 1GWPA 5HGKA 2XGVA 4QNBA 1D1DA 1AK4C 2V4XA 4J93A 4XROA 2PWMA 2XGYA 1M9CC 1M9FC 1P7NA 2Y4ZA 2M8NA 2PWOA 2JPRA 4U0CA 1QRJA 3P05A 2M8PA 2KGFA 3MGEA 4XFXA 4U0EA 4B4NA 1M9YC 2WLVB
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 4U0D A;  4PH3 A;  2PXR C;  4HTW A;  4WYM A;  2GOL B;  4XFY A;  1E6J P;  5HGO A;  1M9X C;  3BP9 A;  1U7K A;  2LF4 A;  4PH0 A;  1G03 A;  4U0B A;  3H4E A;  4DGE C;  4E91 A;  4E92 A;  4LQW C;  2M8L A;  1M9E C;  2WLV A;  4XRQ A;  5HGN A;  2X2D D;  3NTE A;  5JPA A;  1AFV A;  5HGM A;  2GON A;  2X83 A;  4PH2 A;  4U0A A;  2EIA A;  2X82 A;  2XGU A;  4NX4 C;  4U0F A;  4DGA C;  5HGL A;  4XFZ A;  1M9D C;  2XDE A;  1EM9 A;  1EIA A;  3H47 A;  1L6N A;  4INB A;  1GWP A;  5HGK A;  2XGV A;  4QNB A;  1D1D A;  1AK4 C;  2V4X A;  4J93 A;  4XRO A;  2PWM A;  2XGY A;  1M9C C;  1M9F C;  1P7N A;  2Y4Z A;  2M8N A;  2PWO A;  2JPR A;  4U0C A;  1QRJ A;  3P05 A;  2M8P A;  2KGF A;  3MGE A;  4XFX A;  4U0E A;  4B4N A;  1M9Y C;  2WLV B; 
#chains in the Genus database with same CATH topology
 4U0D A;  4PH3 A;  2PXR C;  4HTW A;  4WYM A;  2GOL B;  4XFY A;  1E6J P;  5HGO A;  1M9X C;  3BP9 A;  1U7K A;  2LF4 A;  4PH0 A;  1G03 A;  4U0B A;  3H4E A;  4DGE C;  4E91 A;  4E92 A;  4LQW C;  2M8L A;  1M9E C;  2WLV A;  4XRQ A;  5HGN A;  2X2D D;  3NTE A;  5JPA A;  1AFV A;  5HGM A;  2GON A;  2X83 A;  4PH2 A;  4U0A A;  2EIA A;  2X82 A;  2XGU A;  4NX4 C;  4U0F A;  4DGA C;  5HGL A;  4XFZ A;  1M9D C;  2XDE A;  1EM9 A;  1EIA A;  3H47 A;  1L6N A;  4INB A;  1GWP A;  5HGK A;  2XGV A;  4QNB A;  1D1D A;  1AK4 C;  2V4X A;  4J93 A;  4XRO A;  2PWM A;  2XGY A;  1M9C C;  1M9F C;  1P7N A;  2Y4Z A;  2M8N A;  2PWO A;  2JPR A;  4U0C A;  1QRJ A;  3P05 A;  2M8P A;  2KGF A;  3MGE A;  4XFX A;  4U0E A;  4B4N A;  1M9Y C;  2WLV B; 
#chains in the Genus database with same CATH homology
 4U0D A;  4PH3 A;  2PXR C;  4HTW A;  4WYM A;  2GOL B;  4XFY A;  1E6J P;  5HGO A;  1M9X C;  3BP9 A;  1U7K A;  2LF4 A;  4PH0 A;  1G03 A;  4U0B A;  3H4E A;  4DGE C;  4E91 A;  4E92 A;  4LQW C;  2M8L A;  1M9E C;  2WLV A;  4XRQ A;  5HGN A;  2X2D D;  3NTE A;  5JPA A;  1AFV A;  5HGM A;  2GON A;  2X83 A;  4PH2 A;  4U0A A;  2EIA A;  2X82 A;  2XGU A;  4NX4 C;  4U0F A;  4DGA C;  5HGL A;  4XFZ A;  1M9D C;  2XDE A;  1EM9 A;  1EIA A;  3H47 A;  1L6N A;  4INB A;  1GWP A;  5HGK A;  2XGV A;  4QNB A;  1D1D A;  1AK4 C;  2V4X A;  4J93 A;  4XRO A;  2PWM A;  2XGY A;  1M9C C;  1M9F C;  1P7N A;  2Y4Z A;  2M8N A;  2PWO A;  2JPR A;  4U0C A;  1QRJ A;  3P05 A;  2M8P A;  2KGF A;  3MGE A;  4XFX A;  4U0E A;  4B4N A;  1M9Y C;  2WLV B; 
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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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