2GOLB

Xray structure of gag278
Total Genus 49

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
49
sequence length
135
structure length
135
Chain Sequence
HQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKRWIILGLNKIVRMYS
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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.


  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 Matrix protein p17 (MA)
molecule tags Viral protein
source organism Human immunodeficiency virus 1
total genus 49
structure length 135
sequence length 135
chains with identical sequence D
ec nomenclature
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 2golB00
2KGFA 5HGMA 4PH0A 4XFYA 4B4NA 4XFZA 4XROA 5HGOA 2XGUA 4DGAC 2XGYA 4HTWA 1L6NA 2X82A 4U0EA 2X83A 2GOLB 1D1DA 2XDEA 3NTEA 4U0CA 2M8NA 4U0BA 1AFVA 3MGEA 1G03A 2V4XA 1EIAA 1P7NA 1E6JP 4J93A 1GWPA 1M9YC 3H47A 4U0AA 2XGVA 2PXRC 4PH2A 1M9DC 2WLVB 4DGEC 4E92A 2JPRA 3BP9A 3H4EA 2GONA 4E91A 3P05A 1QRJA 4NX4C 2LF4A 2X2DD 4INBA 1M9EC 2M8PA 2WLVA 4U0DA 5HGLA 2PWOA 1M9FC 2EIAA 4LQWC 5HGNA 4U0FA 2PWMA 2Y4ZA 2M8LA 4XRQA 1AK4C 4XFXA 5JPAA 1U7KA 4PH3A 4WYMA 5HGKA 4QNBA 1M9CC 1EM9A 1M9XC
chains in the Genus database with same CATH superfamily
2KGFA 5HGMA 4PH0A 4XFYA 4B4NA 4XFZA 4XROA 5HGOA 2XGUA 4DGAC 2XGYA 4HTWA 1L6NA 2X82A 4U0EA 2X83A 2GOLB 1D1DA 2XDEA 3NTEA 4U0CA 2M8NA 4U0BA 1AFVA 3MGEA 1G03A 2V4XA 1EIAA 1P7NA 1E6JP 4J93A 1GWPA 1M9YC 3H47A 4U0AA 2XGVA 2PXRC 4PH2A 1M9DC 2WLVB 4DGEC 4E92A 2JPRA 3BP9A 3H4EA 2GONA 4E91A 3P05A 1QRJA 4NX4C 2LF4A 2X2DD 4INBA 1M9EC 2M8PA 2WLVA 4U0DA 5HGLA 2PWOA 1M9FC 2EIAA 4LQWC 5HGNA 4U0FA 2PWMA 2Y4ZA 2M8LA 4XRQA 1AK4C 4XFXA 5JPAA 1U7KA 4PH3A 4WYMA 5HGKA 4QNBA 1M9CC 1EM9A 1M9XC
chains in the Genus database with same CATH topology
2KGFA 5HGMA 4PH0A 4XFYA 4B4NA 4XFZA 4XROA 5HGOA 2XGUA 4DGAC 2XGYA 4HTWA 1L6NA 2X82A 4U0EA 2X83A 2GOLB 1D1DA 2XDEA 3NTEA 4U0CA 2M8NA 4U0BA 1AFVA 3MGEA 1G03A 2V4XA 1EIAA 1P7NA 1E6JP 4J93A 1GWPA 1M9YC 3H47A 4U0AA 2XGVA 2PXRC 4PH2A 1M9DC 2WLVB 4DGEC 4E92A 2JPRA 3BP9A 3H4EA 2GONA 4E91A 3P05A 1QRJA 4NX4C 2LF4A 2X2DD 4INBA 1M9EC 2M8PA 2WLVA 4U0DA 5HGLA 2PWOA 1M9FC 2EIAA 4LQWC 5HGNA 4U0FA 2PWMA 2Y4ZA 2M8LA 4XRQA 1AK4C 4XFXA 5JPAA 1U7KA 4PH3A 4WYMA 5HGKA 4QNBA 1M9CC 1EM9A 1M9XC
chains in the Genus database with same CATH homology

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