2F4QA

Crystal structure of deinococcus radiodurans topoisomerase ib
Total Genus 98
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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
98
sequence length
336
structure length
309
Chain Sequence
PSRTELLAEEYLRREPQKFRLARIARLAVPPAYQDVYVSPDAENELQAFGRDAAGRLQYRYHPDFVQAGALKKWQRLTRFAGALPTLKVATTADLRASGLPPRKVMALMTRLLHVARFRVTYGLSTLRQRHVVVDGNTVTFRFKGKHGVSQHKATSDRTLAANMQKLLDLPGPWLFQTVDAGGGERRRIHSTELNAYLREVIGPFTAKDFRTWGGTLLAAEYLAQQGTESSERQAKKVLVDCVKFVADDLGNTPAVTRGSYICPVIFDRYLDGKVLDDYEPRTERQEAELEGLTRSEGALKRMLESERT
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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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publication title Crystal structure of a bacterial type IB DNA topoisomerase reveals a preassembled active site in the absence of DNA.
pubmed doi rcsb
molecule tags Isomerase
source organism Deinococcus radiodurans
molecule keywords type I topoisomerase, putative
total genus 98
structure length 309
sequence length 336
ec nomenclature
pdb deposition date 2005-11-23

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF01028 Topoisom_I Eukaryotic DNA topoisomerase I, catalytic core
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
1.10.132.120 Mainly Alpha Orthogonal Bundle Topoisomerase I; Chain A, domain 4 Topoisomerase I; Chain A, domain 4 2f4qA02
3.30.66.10 Alpha Beta 2-Layer Sandwich Viral Topoisomerase I DNA topoisomerase I domain 2f4qA01
3.90.15.10 Alpha Beta Alpha-Beta Complex Topoisomerase I; Chain A, domain 3 Topoisomerase I; Chain A, domain 3 2f4qA03
3M4AA 1A35A 1A36A 1VCCA 1A41A 1T8IA 1K4TA 1R49A 1RRJA 3IGCA 1SC7A 1EJ9A 2H7FX 2F4QA 1A31A 1NH3A 1SEUA 1TL8A 1LPQA 2H7GX 1K4SA 2B9SA 1RR8C
chains in the Genus database with same CATH superfamily
2A6HD 3M4AA 1ISEA 1EH1A 4AHCA 1GE9A 4GFQA 2E2HA 3GTQA 2VUMA 1VCCA 4JLRC 1IW7D 1A41A 2R7ZA 1YNND 3P9AA 1I6VD 4KB4A 4AYBA 1WQHA 1Y1WA 5MLC9 2NVXA 1TWHA 1K4TA 1A31A 5C9HA 1TL8A 1LPQA 1K83A 3CQZA 1MIUA 2A68D 2NVYA 1I3QA 4D3YA 2R93A 3K57A 1R9TA 4LMOA 2BE5D 2JA6A 4F3EA 4FGUA 4NOKA 4D3ZA 3K58A 1TWGA 1EJ9A 4FYDA 3IAYA 1SMYD 2F4QA 3MAQA 2JA5A 1NH3A 5CQGA 3LF9A 3KYLA 2WAQA 1TWFA 2A6ED 4AN8A 1I50A 1YNJD 1IS1A 3LHPS 1EK8A 1RR8C 3GTLA 3HKZA 2A69D 3GTKA 4Q5GA 3GTGA 1Y698 4IP9A 1TWCA 2Y0SA 5JSBB 3GTJA 1TWAA 2PMZA 4H3TA 2R92A 2WB1A 4NOLA 1ZYRD 4IP8A 1R49A 1RRJA 2O5JD 1TGOA 3IGCA 3FKIA 3K59A 2CW0D 2B63A 2H7FX 1WCMA 1SEUA 4QIWA 1R5ZA 2H7GX 3GTOA 5JSNB 4KDDA 1K4SA 2JA7A 4EJ3A 2B9SA 4NOMA 4KB2A 3K5NA 4OYDB 1SFOA 1A35A 3DU5A 1Q8IA 3K5LA 2E2IA 1A36A 1WQGA 1Y1VA 4C2MA 3WVOA 3SJRA 4O26A 4Q5VA 4KC6A 2B9SB 1DD5A 2R4GA 2YU9A 1T8IA 1SC7A 3GTPA 1HQMD 4FXDA 4KAWX 4L8IA 3K5MA 3DU6A 1WQFA 3K5OA 3GTMA 1V9MA 3H0GA 4QCLA
chains in the Genus database with same CATH topology
2A6HD 3M4AA 1ISEA 1EH1A 4AHCA 1GE9A 4GFQA 2E2HA 3GTQA 2VUMA 1VCCA 4JLRC 1IW7D 1A41A 2R7ZA 1YNND 3P9AA 1I6VD 4KB4A 4AYBA 1WQHA 1Y1WA 5MLC9 2NVXA 1TWHA 1K4TA 1A31A 5C9HA 1TL8A 1LPQA 1K83A 3CQZA 1MIUA 2A68D 2NVYA 1I3QA 4D3YA 2R93A 3K57A 1R9TA 4LMOA 2BE5D 2JA6A 4F3EA 4FGUA 4NOKA 4D3ZA 3K58A 1TWGA 1EJ9A 4FYDA 3IAYA 1SMYD 2F4QA 3MAQA 2JA5A 1NH3A 5CQGA 3LF9A 3KYLA 2WAQA 1TWFA 2A6ED 4AN8A 1I50A 1YNJD 1IS1A 3LHPS 1EK8A 1RR8C 3GTLA 3HKZA 2A69D 3GTKA 4Q5GA 3GTGA 1Y698 4IP9A 1TWCA 2Y0SA 5JSBB 3GTJA 1TWAA 2PMZA 4H3TA 2R92A 2WB1A 4NOLA 1ZYRD 4IP8A 1R49A 1RRJA 2O5JD 1TGOA 3IGCA 3FKIA 3K59A 2CW0D 2B63A 2H7FX 1WCMA 1SEUA 4QIWA 1R5ZA 2H7GX 3GTOA 5JSNB 4KDDA 1K4SA 2JA7A 4EJ3A 2B9SA 4NOMA 4KB2A 3K5NA 4OYDB 1SFOA 1A35A 3DU5A 1Q8IA 3K5LA 2E2IA 1A36A 1WQGA 1Y1VA 4C2MA 3WVOA 3SJRA 4O26A 4Q5VA 4KC6A 2B9SB 1DD5A 2R4GA 2YU9A 1T8IA 1SC7A 3GTPA 1HQMD 4FXDA 4KAWX 4L8IA 3K5MA 3DU6A 1WQFA 3K5OA 3GTMA 1V9MA 3H0GA 4QCLA
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 3M4A A;  1A35 A;  1A36 A;  1VCC A;  1A41 A;  1T8I A;  1K4T A;  1R49 A;  1RRJ A;  3IGC A;  1SC7 A;  1EJ9 A;  2H7F X;  2F4Q A;  1A31 A;  1NH3 A;  1SEU A;  1TL8 A;  1LPQ A;  2H7G X;  1K4S A;  2B9S A;  1RR8 C; 
#chains in the Genus database with same CATH topology
 2A6H D;  3M4A A;  1ISE A;  1EH1 A;  4AHC A;  1GE9 A;  4GFQ A;  2E2H A;  3GTQ A;  2VUM A;  1VCC A;  4JLR C;  1IW7 D;  1A41 A;  2R7Z A;  1YNN D;  3P9A A;  1I6V D;  4KB4 A;  4AYB A;  1WQH A;  1Y1W A;  5MLC 9;  2NVX A;  1TWH A;  1K4T A;  1A31 A;  5C9H A;  1TL8 A;  1LPQ A;  1K83 A;  3CQZ A;  1MIU A;  2A68 D;  2NVY A;  1I3Q A;  4D3Y A;  2R93 A;  3K57 A;  1R9T A;  4LMO A;  2BE5 D;  2JA6 A;  4F3E A;  4FGU A;  4NOK A;  4D3Z A;  3K58 A;  1TWG A;  1EJ9 A;  4FYD A;  3IAY A;  1SMY D;  2F4Q A;  3MAQ A;  2JA5 A;  1NH3 A;  5CQG A;  3LF9 A;  3KYL A;  2WAQ A;  1TWF A;  2A6E D;  4AN8 A;  1I50 A;  1YNJ D;  1IS1 A;  3LHP S;  1EK8 A;  1RR8 C;  3GTL A;  3HKZ A;  2A69 D;  3GTK A;  4Q5G A;  3GTG A;  1Y69 8;  4IP9 A;  1TWC A;  2Y0S A;  5JSB B;  3GTJ A;  1TWA A;  2PMZ A;  4H3T A;  2R92 A;  2WB1 A;  4NOL A;  1ZYR D;  4IP8 A;  1R49 A;  1RRJ A;  2O5J D;  1TGO A;  3IGC A;  3FKI A;  3K59 A;  2CW0 D;  2B63 A;  2H7F X;  1WCM A;  1SEU A;  4QIW A;  1R5Z A;  2H7G X;  3GTO A;  5JSN B;  4KDD A;  1K4S A;  2JA7 A;  4EJ3 A;  2B9S A;  4NOM A;  4KB2 A;  3K5N A;  4OYD B;  1SFO A;  1A35 A;  3DU5 A;  1Q8I A;  3K5L A;  2E2I A;  1A36 A;  1WQG A;  1Y1V A;  4C2M A;  3WVO A;  3SJR A;  4O26 A;  4Q5V A;  4KC6 A;  2B9S B;  1DD5 A;  2R4G A;  2YU9 A;  1T8I A;  1SC7 A;  3GTP A;  1HQM D;  4FXD A;  4KAW X;  4L8I A;  3K5M A;  3DU6 A;  1WQF A;  3K5O A;  3GTM A;  1V9M A;  3H0G A;  4QCL A; 
#chains in the Genus database with same CATH homology
 2A6H D;  3M4A A;  1ISE A;  1EH1 A;  4AHC A;  1GE9 A;  4GFQ A;  2E2H A;  3GTQ A;  2VUM A;  1VCC A;  4JLR C;  1IW7 D;  1A41 A;  2R7Z A;  1YNN D;  3P9A A;  1I6V D;  4KB4 A;  4AYB A;  1WQH A;  1Y1W A;  5MLC 9;  2NVX A;  1TWH A;  1K4T A;  1A31 A;  5C9H A;  1TL8 A;  1LPQ A;  1K83 A;  3CQZ A;  1MIU A;  2A68 D;  2NVY A;  1I3Q A;  4D3Y A;  2R93 A;  3K57 A;  1R9T A;  4LMO A;  2BE5 D;  2JA6 A;  4F3E A;  4FGU A;  4NOK A;  4D3Z A;  3K58 A;  1TWG A;  1EJ9 A;  4FYD A;  3IAY A;  1SMY D;  2F4Q A;  3MAQ A;  2JA5 A;  1NH3 A;  5CQG A;  3LF9 A;  3KYL A;  2WAQ A;  1TWF A;  2A6E D;  4AN8 A;  1I50 A;  1YNJ D;  1IS1 A;  3LHP S;  1EK8 A;  1RR8 C;  3GTL A;  3HKZ A;  2A69 D;  3GTK A;  4Q5G A;  3GTG A;  1Y69 8;  4IP9 A;  1TWC A;  2Y0S A;  5JSB B;  3GTJ A;  1TWA A;  2PMZ A;  4H3T A;  2R92 A;  2WB1 A;  4NOL A;  1ZYR D;  4IP8 A;  1R49 A;  1RRJ A;  2O5J D;  1TGO A;  3IGC A;  3FKI A;  3K59 A;  2CW0 D;  2B63 A;  2H7F X;  1WCM A;  1SEU A;  4QIW A;  1R5Z A;  2H7G X;  3GTO A;  5JSN B;  4KDD A;  1K4S A;  2JA7 A;  4EJ3 A;  2B9S A;  4NOM A;  4KB2 A;  3K5N A;  4OYD B;  1SFO A;  1A35 A;  3DU5 A;  1Q8I A;  3K5L A;  2E2I A;  1A36 A;  1WQG A;  1Y1V A;  4C2M A;  3WVO A;  3SJR A;  4O26 A;  4Q5V A;  4KC6 A;  2B9S B;  1DD5 A;  2R4G A;  2YU9 A;  1T8I A;  1SC7 A;  3GTP A;  1HQM D;  4FXD A;  4KAW X;  4L8I A;  3K5M A;  3DU6 A;  1WQF A;  3K5O A;  3GTM A;  1V9M A;  3H0G A;  4QCL 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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