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
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 tags Viral protein
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
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
1M9XC 1AK4C 4U0EA 2M8NA 4XFXA 4B4NA 1M9FC 4QNBA 4INBA 4XFZA 1D1DA 1EIAA 3NTEA 2X83A 1E6JP 1L6NA 1QRJA 4HTWA 2JPRA 3BP9A 2PWMA 2GONA 1G03A 5HGKA 2X2DD 1M9EC 3P05A 2WLVA 4U0BA 4XRQA 1P7NA 2WLVB 1AFVA 2LF4A 4U0CA 2Y4ZA 2V4XA 4PH3A 4E91A 1M9DC 1M9YC 4DGEC 2XGVA 5HGNA 4E92A 4PH0A 4NX4C 1GWPA 2M8PA 5HGOA 1U7KA 4DGAC 5HGLA 2PWOA 4U0AA 2XGUA 4U0DA 3H4EA 4XROA 1EM9A 4J93A 2EIAA 4PH2A 2XGYA 1M9CC 4XFYA 4U0FA 2M8LA 3MGEA 3H47A 4LQWC 2X82A 2XDEA 5JPAA 2GOLB 4WYMA 2PXRC 2KGFA 5HGMA
chains in the Genus database with same CATH superfamily
1M9XC 1AK4C 4U0EA 2M8NA 4XFXA 4B4NA 1M9FC 4QNBA 4INBA 4XFZA 1D1DA 1EIAA 3NTEA 2X83A 1E6JP 1L6NA 1QRJA 4HTWA 2JPRA 3BP9A 2PWMA 2GONA 1G03A 5HGKA 2X2DD 1M9EC 3P05A 2WLVA 4U0BA 4XRQA 1P7NA 2WLVB 1AFVA 2LF4A 4U0CA 2Y4ZA 2V4XA 4PH3A 4E91A 1M9DC 1M9YC 4DGEC 2XGVA 5HGNA 4E92A 4PH0A 4NX4C 1GWPA 2M8PA 5HGOA 1U7KA 4DGAC 5HGLA 2PWOA 4U0AA 2XGUA 4U0DA 3H4EA 4XROA 1EM9A 4J93A 2EIAA 4PH2A 2XGYA 1M9CC 4XFYA 4U0FA 2M8LA 3MGEA 3H47A 4LQWC 2X82A 2XDEA 5JPAA 2GOLB 4WYMA 2PXRC 2KGFA 5HGMA
chains in the Genus database with same CATH topology
1M9XC 1AK4C 4U0EA 2M8NA 4XFXA 4B4NA 1M9FC 4QNBA 4INBA 4XFZA 1D1DA 1EIAA 3NTEA 2X83A 1E6JP 1L6NA 1QRJA 4HTWA 2JPRA 3BP9A 2PWMA 2GONA 1G03A 5HGKA 2X2DD 1M9EC 3P05A 2WLVA 4U0BA 4XRQA 1P7NA 2WLVB 1AFVA 2LF4A 4U0CA 2Y4ZA 2V4XA 4PH3A 4E91A 1M9DC 1M9YC 4DGEC 2XGVA 5HGNA 4E92A 4PH0A 4NX4C 1GWPA 2M8PA 5HGOA 1U7KA 4DGAC 5HGLA 2PWOA 4U0AA 2XGUA 4U0DA 3H4EA 4XROA 1EM9A 4J93A 2EIAA 4PH2A 2XGYA 1M9CC 4XFYA 4U0FA 2M8LA 3MGEA 3H47A 4LQWC 2X82A 2XDEA 5JPAA 2GOLB 4WYMA 2PXRC 2KGFA 5HGMA
chains in the Genus database with same CATH homology


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