2XI1A

Crystal structure of the hiv-1 nef sequenced from a patient's sample
Total Genus 28
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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
28
sequence length
130
structure length
101
Chain Sequence
VPLRPMTYKGAVDLSFFLKEKGGLEGLVYSQREKEILDLWVYHTQGYFPDWQCYTPGPGVRYPLTFGWCFKLVPVDEVLKWKFDSHLAHTHMARELHPEYF
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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 NEF
publication title A Novel Dimer-Tetramer Transition Captured by the Crystal Structure of the HIV-1 Nef.
pubmed doi rcsb
source organism Human immunodeficiency virus type 1 (bh5 isolate)
total genus 28
structure length 101
sequence length 130
ec nomenclature
pdb deposition date 2010-06-25

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF00469 F-protein Negative factor, (F-Protein) or Nef
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
3.30.62.10 Alpha Beta 2-Layer Sandwich Nef Regulatory Factor Nef Regulatory Factor 2xi1A00
1AVZA 1EFNB 3REBA 2XI1B 3RBBA 1AVVA 3IK5A 3REAA 4D8DB 4EN2B 4EMZB 4NEEC 2XI1A 4ORZB 2NEFA 3IOZA 4U5WA
chains in the Genus database with same CATH superfamily
1AVZA 1EFNB 3REBA 2XI1B 3RBBA 1AVVA 3IK5A 3REAA 4D8DB 4EN2B 4EMZB 4NEEC 2XI1A 4ORZB 2NEFA 3IOZA 4U5WA
chains in the Genus database with same CATH topology
1AVZA 1EFNB 3REBA 2XI1B 3RBBA 1AVVA 3IK5A 3REAA 4D8DB 4EN2B 4EMZB 4NEEC 2XI1A 4ORZB 2NEFA 3IOZA 4U5WA
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 1AVZ A;  1EFN B;  3REB A;  2XI1 B;  3RBB A;  1AVV A;  3IK5 A;  3REA A;  4D8D B;  4EN2 B;  4EMZ B;  4NEE C;  2XI1 A;  4ORZ B;  2NEF A;  3IOZ A;  4U5W A; 
#chains in the Genus database with same CATH topology
 1AVZ A;  1EFN B;  3REB A;  2XI1 B;  3RBB A;  1AVV A;  3IK5 A;  3REA A;  4D8D B;  4EN2 B;  4EMZ B;  4NEE C;  2XI1 A;  4ORZ B;  2NEF A;  3IOZ A;  4U5W A; 
#chains in the Genus database with same CATH homology
 1AVZ A;  1EFN B;  3REB A;  2XI1 B;  3RBB A;  1AVV A;  3IK5 A;  3REA A;  4D8D B;  4EN2 B;  4EMZ B;  4NEE C;  2XI1 A;  4ORZ B;  2NEF A;  3IOZ A;  4U5W 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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#similar chains in the pdb database (?% sequence similarity)
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