2QSGA

Crystal structure of rad4-rad23 bound to a uv-damaged dna
Total Genus 147
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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
147
sequence length
510
structure length
502
Chain Sequence
DARRTSRNVCSNEERKRRKYFHMLYLVCLMVHGFIRNEWINSKRLSRKLSNLVPEKVFELLHPQKDEELPLRSTRKLLDGLKKCMELWQKHWKITKKYDNEGLYMRTWKEIEMSANNKRKFKTLKRSDFLRAVSKGHGDPDISVQGFVAMLRACNVNARLIMSCQPPDFTNMKIDTSLNGNNAYKDMVKYPIFWCEVWDKFSKKWITVDPVNLKTIEQVRLHSKLAPKGVACCERNMLRYVIAYDRKYGCRDVTRRYAQWMNSKVRKRRITKDDFGEKWFRKVITALHHRKRTKIDDYEDQYFFQRDESEGIPDSVQDLKNHPYYVLEQDIKQTQIVKPGCKECGYLKVHGKVGKVLKVYAKRDIADLKSARQWYMNGRILKTGSRCKKVIKRTVEEDERLYSFEDTELYIPPLASASGEITKNTFGNIEVFAPTMIPGNCCLVENPVAIKAARFLGVEFAPAVTSFKFERGSTVKPVLSGIVVAKWLREAIETAIDGIEFI
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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 Dna binding protein/dna
molecule keywords native strand of the CPD-mismatch DNA
publication title Recognition of DNA damage by the Rad4 nucleotide excision repair protein
pubmed doi rcsb
source organism Saccharomyces cerevisiae
total genus 147
structure length 502
sequence length 510
ec nomenclature
pdb deposition date 2007-07-31

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF03835 Rad4 Rad4 transglutaminase-like domain
A PF10403 BHD_1 Rad4 beta-hairpin domain 1
A PF10405 BHD_3 Rad4 beta-hairpin domain 3
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
2.20.20.110 Mainly Beta Single Sheet Anthopleurin-A Anthopleurin-A 2qsgA02
2.20.20.120 Mainly Beta Single Sheet Anthopleurin-A Anthopleurin-A 2qsgA03
3.90.260.10 Alpha Beta Alpha-Beta Complex Coagulation Factor XIII; Chain A, domain 2 Transglutaminase-like 2qsgA01
1QRKA 1FIEA 1NUDA 1GGTA 1L9MA 2QSGA 1EX0A 2QSFA 1L9NA 3S3SA 4KTYA 4YIRA 1KV3A 2QSHA 1F13A 1G0DA 1GGUA 1EVUA 1GGYA 4PYGA 1NUGA 1NUFA 3S3PA 2Q3ZA 3S3JA 3LY6A
chains in the Genus database with same CATH superfamily
2SH1A 1AHLA 1ZUFA 1FIEA 4GV5A 1NUDA 1WQKA 1QRKA 3C30A 1Z99A 1GGTA 2MUBA 1ZHHB 1L9MA 2QSGA 1EX0A 2QSFA 1L9NA 3MYVA 3S3SA 2H9XA 1ZLHB 2IKDA 4KTYA 3C38A 4YIRA 2MN3A 3IF4A 2HJ9C 1KV3A 2B9KA 2QSHA 3D4UB 3KEZA 1ATXA 1ZUEA 1F13A 2RNGA 1G0DA 3LY6A 1GGUA 2JTOA 1EVUA 1ZLIB 1D6BA 1WXNA 1GGYA 2XXLA 1APFA 4PYGA 1H5OA 1BDSA 3LMSB 1NUFA 1NUGA 2IKEA 2K2XA 1SH1A 2Q3ZA 3S3PA 1GKUB 2BDSA 1GL9B 3MCXA 1SHIA 3S3JA 2JR3A 1EL6A 2DLAA 1B8WA 2HJEA
chains in the Genus database with same CATH topology
2SH1A 1AHLA 1ZUFA 1FIEA 4GV5A 1NUDA 1WQKA 1QRKA 3C30A 1Z99A 1GGTA 2MUBA 1ZHHB 1L9MA 2QSGA 1EX0A 2QSFA 1L9NA 3MYVA 3S3SA 2H9XA 1ZLHB 2IKDA 4KTYA 3C38A 4YIRA 2MN3A 2HJ9C 1KV3A 2B9KA 2QSHA 3D4UB 3KEZA 1ATXA 1ZUEA 1F13A 2RNGA 1G0DA 3LY6A 1GGUA 2JTOA 1EVUA 1ZLIB 1GGYA 1WXNA 2XXLA 1APFA 4PYGA 1H5OA 1BDSA 3LMSB 1NUFA 1NUGA 2IKEA 2K2XA 1SH1A 2Q3ZA 3S3PA 2BDSA 3MCXA 1SHIA 3S3JA 2JR3A 1D6BA 2DLAA 1B8WA 2HJEA
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 1QRK A;  1FIE A;  1NUD A;  1GGT A;  1L9M A;  2QSG A;  1EX0 A;  2QSF A;  1L9N A;  3S3S A;  4KTY A;  4YIR A;  1KV3 A;  2QSH A;  1F13 A;  1G0D A;  1GGU A;  1EVU A;  1GGY A;  4PYG A;  1NUG A;  1NUF A;  3S3P A;  2Q3Z A;  3S3J A;  3LY6 A; 
#chains in the Genus database with same CATH topology
 2SH1 A;  1AHL A;  1ZUF A;  1FIE A;  4GV5 A;  1NUD A;  1WQK A;  1QRK A;  3C30 A;  1Z99 A;  1GGT A;  2MUB A;  1ZHH B;  1L9M A;  2QSG A;  1EX0 A;  2QSF A;  1L9N A;  3MYV A;  3S3S A;  2H9X A;  1ZLH B;  2IKD A;  4KTY A;  3C38 A;  4YIR A;  2MN3 A;  3IF4 A;  2HJ9 C;  1KV3 A;  2B9K A;  2QSH A;  3D4U B;  3KEZ A;  1ATX A;  1ZUE A;  1F13 A;  2RNG A;  1G0D A;  3LY6 A;  1GGU A;  2JTO A;  1EVU A;  1ZLI B;  1D6B A;  1WXN A;  1GGY A;  2XXL A;  1APF A;  4PYG A;  1H5O A;  1BDS A;  3LMS B;  1NUF A;  1NUG A;  2IKE A;  2K2X A;  1SH1 A;  2Q3Z A;  3S3P A;  1GKU B;  2BDS A;  1GL9 B;  3MCX A;  1SHI A;  3S3J A;  2JR3 A;  1EL6 A;  2DLA A;  1B8W A;  2HJE A; 
#chains in the Genus database with same CATH homology
 2SH1 A;  1AHL A;  1ZUF A;  1FIE A;  4GV5 A;  1NUD A;  1WQK A;  1QRK A;  3C30 A;  1Z99 A;  1GGT A;  2MUB A;  1ZHH B;  1L9M A;  2QSG A;  1EX0 A;  2QSF A;  1L9N A;  3MYV A;  3S3S A;  2H9X A;  1ZLH B;  2IKD A;  4KTY A;  3C38 A;  4YIR A;  2MN3 A;  2HJ9 C;  1KV3 A;  2B9K A;  2QSH A;  3D4U B;  3KEZ A;  1ATX A;  1ZUE A;  1F13 A;  2RNG A;  1G0D A;  3LY6 A;  1GGU A;  2JTO A;  1EVU A;  1ZLI B;  1GGY A;  1WXN A;  2XXL A;  1APF A;  4PYG A;  1H5O A;  1BDS A;  3LMS B;  1NUF A;  1NUG A;  2IKE A;  2K2X A;  1SH1 A;  2Q3Z A;  3S3P A;  2BDS A;  3MCX A;  1SHI A;  3S3J A;  2JR3 A;  1D6B A;  2DLA A;  1B8W A;  2HJE 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)

 
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#similar chains, but unknotted
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