2GONA

Xray structure of gag133-278
Total Genus 41
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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
41
sequence length
135
structure length
127
Chain Sequence
HQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHPVHMREPRGSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKRWIILGLNKIVRMYS

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.


  Genus data interpretation
publication title Implications for Viral Capsid Assembly from Crystal Structures of HIV-1 Gag 1-278 and CAN 133-278.
pubmed doi rcsb
molecule keywords Capsid protein p24 (CA)
molecule tags Viral protein
source organism Human immunodeficiency virus 1
total genus 41
structure length 127
sequence length 135
chains with identical sequence B, C, D
ec nomenclature ec 2.7.7.49: RNA-directed DNA polymerase.
pdb deposition date 2006-04-13
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 2gonA00
4U0AA 4U0BA 2WLVB 4PH2A 2GOLB 4WYMA 4DGEC 4XFXA 5HGKA 4E92A 1AFVA 1M9FC 2M8PA 2XGUA 4PH0A 1U7KA 2M8NA 2PWMA 2Y4ZA 5HGLA 2KGFA 4PH3A 4LQWC 3H4EA 1AK4C 2XGVA 1D1DA 4B4NA 2GONA 2PWOA 2XGYA 1E6JP 3NTEA 1GWPA 4XFZA 1G03A 1M9DC 4DGAC 3BP9A 4U0FA 1M9XC 2PXRC 1EIAA 5HGNA 1M9YC 1M9EC 4XRQA 5JPAA 4U0CA 2XDEA 2X83A 5HGMA 1L6NA 1P7NA 4NX4C 4E91A 2X2DD 3H47A 4U0EA 2M8LA 2WLVA 4J93A 2LF4A 4INBA 4U0DA 1M9CC 4XROA 5HGOA 4QNBA 4XFYA 1EM9A 3P05A 2EIAA 1QRJA 3MGEA 4HTWA 2X82A 2JPRA 2V4XA
chains in the Genus database with same CATH superfamily
4U0AA 4U0BA 2WLVB 4PH2A 2GOLB 4WYMA 4DGEC 4XFXA 5HGKA 4E92A 1AFVA 1M9FC 2M8PA 2XGUA 4PH0A 1U7KA 2M8NA 2PWMA 2Y4ZA 5HGLA 2KGFA 4PH3A 4LQWC 3H4EA 1AK4C 2XGVA 1D1DA 4B4NA 2GONA 2PWOA 2XGYA 1E6JP 3NTEA 1GWPA 4XFZA 1G03A 1M9DC 4DGAC 3BP9A 4U0FA 1M9XC 2PXRC 1EIAA 5HGNA 1M9YC 1M9EC 4XRQA 5JPAA 4U0CA 2XDEA 2X83A 5HGMA 1L6NA 1P7NA 4NX4C 4E91A 2X2DD 3H47A 4U0EA 2M8LA 2WLVA 4J93A 2LF4A 4INBA 4U0DA 1M9CC 4XROA 5HGOA 4QNBA 4XFYA 1EM9A 3P05A 2EIAA 1QRJA 3MGEA 4HTWA 2X82A 2JPRA 2V4XA
chains in the Genus database with same CATH topology
4U0AA 4U0BA 2WLVB 4PH2A 2GOLB 4WYMA 4DGEC 4XFXA 5HGKA 4E92A 1AFVA 1M9FC 2M8PA 2XGUA 4PH0A 1U7KA 2M8NA 2PWMA 2Y4ZA 5HGLA 2KGFA 4PH3A 4LQWC 3H4EA 1AK4C 2XGVA 1D1DA 4B4NA 2GONA 2PWOA 2XGYA 1E6JP 3NTEA 1GWPA 4XFZA 1G03A 1M9DC 4DGAC 3BP9A 4U0FA 1M9XC 2PXRC 1EIAA 5HGNA 1M9YC 1M9EC 4XRQA 5JPAA 4U0CA 2XDEA 2X83A 5HGMA 1L6NA 1P7NA 4NX4C 4E91A 2X2DD 3H47A 4U0EA 2M8LA 2WLVA 4J93A 2LF4A 4INBA 4U0DA 1M9CC 4XROA 5HGOA 4QNBA 4XFYA 1EM9A 3P05A 2EIAA 1QRJA 3MGEA 4HTWA 2X82A 2JPRA 2V4XA
chains in the Genus database with same CATH homology

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