3M4AA

Crystal structure of a bacterial topoisomerase ib in complex with dna reveals a secondary dna binding site
Total Genus 109
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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
109
sequence length
337
structure length
304
Chain Sequence
b'PSRTELLARRARIARLAVPPAYQDVYVSPDAENELQAFGRDAARLQYRYHPDFVALKKWQRLTRFAGALPTLKVATTADLRASGLPPRKVMALMTRLLHVARFRVGSDIYARQHKTYGLSTLRQRHVVVDGNTVTFRFKGKHGVSQHKATSDRTLAANMQKLLDLPGPWLFQTVDAGGERRRIHSTELNAYLREVIGPFTAKDFRTWGGTLLAAEYLAQQGTESSERQAKKVLVDCVKFVADDLGNTPAVTRGSYICPVIFDRYLDGKVLDDYEPRTERQEAELEGLTRSEGALKRMLESERTL'
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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 keywords Putative Type I topoisomerase
publication title Crystal structure of a bacterial topoisomerase IB in complex with DNA reveals a secondary DNA binding site.
pubmed doi rcsb
source organism Deinococcus radiodurans
molecule tags Isomerase/dna
total genus 109
structure length 304
sequence length 337
ec nomenclature
pdb deposition date 2010-03-10

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 3m4aA02
3.30.66.10 Alpha Beta 2-Layer Sandwich Viral Topoisomerase I DNA topoisomerase I domain 3m4aA01
3.90.15.10 Alpha Beta Alpha-Beta Complex Topoisomerase I; Chain A, domain 3 Topoisomerase I; Chain A, domain 3 3m4aA03
1TL8A 1A31A 1RRJA 1A36A 3IGCA 2H7GX 1EJ9A 1R49A 1K4TA 1T8IA 2H7FX 2F4QA 2B9SA 1VCCA 1SC7A 1NH3A 1SEUA 1RR8C 1LPQA 1A35A 1K4SA 3M4AA 1A41A
chains in the Genus database with same CATH superfamily
4KC6A 4Q5GA 1SMYD 3DU5A 3HKZA 3GTKA 1RRJA 1TWCA 2R7ZA 2H7GX 1HQMD 2R4GA 1ZYRD 1TWAA 4QIWA 1SFOA 3K5MA 1V9MA 4H3TA 2O5JD 2F4QA 1WQFA 3GTMA 3K59A 4FYDA 4KDDA 4AYBA 1SC7A 1NH3A 3WVOA 1YNJD 1Y1VA 4KB2A 4OYDB 2R93A 4FGUA 1DD5A 1IW7D 1R9TA 4D3YA 1I6VD 1WQGA 1EK8A 2Y0SA 3IGCA 2H7FX 4F3EA 3K5OA 1MIUA 1TL8A 3IAYA 1A31A 1I3QA 2A6HD 1A36A 1EH1A 3K5NA 3FKIA 4O26A 1IS1A 3CQZA 1R49A 1R5ZA 3GTJA 1TGOA 5CQGA 2B9SB 3GTLA 2WB1A 1SEUA 1RR8C 1Y1WA 1WQHA 3K58A 3GTQA 1WCMA 2CW0D 2JA7A 1A35A 2YU9A 4AN8A 3P9AA 2E2HA 4IP9A 1A41A 5JSNB 4D3ZA 3KYLA 1ISEA 4NOMA 4NOLA 1YNND 2PMZA 4AHCA 1K83A 1VCCA 2B9SA 2R92A 4FXDA 4QCLA 4EJ3A 3LF9A 2A6ED 3GTOA 3GTGA 1TWFA 4C2MA 3M4AA 4GFQA 5C9HA 2A69D 3LHPS 1TWGA 4KAWX 5JSBB 2WAQA 4L8IA 2JA6A 1GE9A 3MAQA 2A68D 2E2IA 1EJ9A 1K4TA 1Q8IA 2BE5D 4NOKA 1T8IA 2JA5A 4LMOA 5MLC9 4Q5VA 1TWHA 4JLRC 1I50A 1Y698 3K57A 3K5LA 3H0GA 2B63A 4KB4A 3SJRA 3GTPA 1LPQA 2VUMA 2NVYA 3DU6A 2NVXA 1K4SA 4IP8A
chains in the Genus database with same CATH topology
4KC6A 4Q5GA 1SMYD 3DU5A 3HKZA 3GTKA 1RRJA 1TWCA 2R7ZA 2H7GX 1HQMD 2R4GA 1ZYRD 1TWAA 4QIWA 1SFOA 3K5MA 1V9MA 4H3TA 2O5JD 2F4QA 1WQFA 3GTMA 3K59A 4FYDA 4KDDA 4AYBA 1SC7A 1NH3A 3WVOA 1YNJD 1Y1VA 4KB2A 4OYDB 2R93A 4FGUA 1DD5A 1IW7D 1R9TA 4D3YA 1I6VD 1WQGA 1EK8A 2Y0SA 3IGCA 2H7FX 4F3EA 3K5OA 1MIUA 1TL8A 3IAYA 1A31A 1I3QA 2A6HD 1A36A 1EH1A 3K5NA 3FKIA 4O26A 1IS1A 3CQZA 1R49A 1R5ZA 3GTJA 1TGOA 5CQGA 2B9SB 3GTLA 2WB1A 1SEUA 1RR8C 1Y1WA 1WQHA 3K58A 3GTQA 1WCMA 2CW0D 2JA7A 1A35A 2YU9A 4AN8A 3P9AA 2E2HA 4IP9A 1A41A 5JSNB 4D3ZA 3KYLA 1ISEA 4NOMA 4NOLA 1YNND 2PMZA 4AHCA 1K83A 1VCCA 2B9SA 2R92A 4FXDA 4QCLA 4EJ3A 3LF9A 2A6ED 3GTOA 3GTGA 1TWFA 4C2MA 3M4AA 4GFQA 5C9HA 2A69D 3LHPS 1TWGA 4KAWX 5JSBB 2WAQA 4L8IA 2JA6A 1GE9A 3MAQA 2A68D 2E2IA 1EJ9A 1K4TA 1Q8IA 2BE5D 4NOKA 1T8IA 2JA5A 4LMOA 5MLC9 4Q5VA 1TWHA 4JLRC 1I50A 1Y698 3K57A 3K5LA 3H0GA 2B63A 4KB4A 3SJRA 3GTPA 1LPQA 2VUMA 2NVYA 3DU6A 2NVXA 1K4SA 4IP8A
chains in the Genus database with same CATH homology


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