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


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