2F4QA

Crystal structure of deinococcus radiodurans topoisomerase ib
Total Genus 98

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

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
EMPTYS2 (22-23)AH2 (39-45)TI2 (59-62)TVIII1 (57-60)S3 (52-56)TI1 (48-51)3H6 (191-197)S4 (64-69)TI3 (70-73)S5 (75-79)TVIII3 (200-203)S9 (205-207)3H1 (81-83)TII1 (85-88)AH9 (282-289)AH10 (292-300)AH3 (91-114)TIV5 (138-151)TI4 (208-211)3H2 (120-122)S7 (166-173)TIV4 (122-126)AH4 (128-134)AH7 (235-254)S6 (160-163)3H4 (157-159)TII'1 (163-166)AH5 (186-190)3H5 (174-176)S8 (177-184)TVIII4 (202-205)S10 (214-216)TVIII5 (211-214)AH8 (260-278)AH6 (219-230)TIV6 (231-234)3H7 (304-307)AH1 (4-10)S1 (13-15)TIV1 (15-21)TVIII2 (62-65)3H3 (152-154)TVIa1 (230-233)Updating...
connected with : NaN
molecule tags Isomerase
source organism Deinococcus radiodurans
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 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
1A41A 1R49A 1EJ9A 1LPQA 2B9SA 3IGCA 2H7FX 1T8IA 1K4SA 1SC7A 2F4QA 2H7GX 1K4TA 1A36A 1VCCA 1RRJA 1A31A 1TL8A 3M4AA 1SEUA 1NH3A 1A35A 1RR8C
chains in the Genus database with same CATH superfamily
2JA7A 1WQHA 3P9AA 2R92A 1Y1VA 4O26A 3GTMA 2E2IA 4GFQA 1T8IA 2NVXA 1DD5A 3HKZA 4OYDB 3DU6A 2F4QA 4D3ZA 1WQFA 4C2MA 2R4GA 4NOMA 5MLC9 1V9MA 1TWAA 1VCCA 3WVOA 3M4AA 2O5JD 1Y1WA 4KB4A 2NVYA 4KC6A 4QIWA 1A41A 2WAQA 3CQZA 4L8IA 4LMOA 1YNND 3K57A 4Q5GA 3GTPA 3K59A 2R7ZA 3K58A 1K4SA 3SJRA 4KDDA 4FXDA 2WB1A 4KAWX 2Y0SA 1RRJA 1TWGA 1TL8A 1GE9A 4AYBA 5C9HA 3GTLA 1TWHA 3DU5A 1I6VD 1IW7D 4Q5VA 4FGUA 1SFOA 1R49A 1ZYRD 2A6HD 1EJ9A 1LPQA 2B9SA 1R9TA 2VUMA 2JA5A 2B63A 1TWCA 3GTKA 4FYDA 2A68D 3GTGA 1MIUA 1K4TA 4NOLA 4KB2A 2CW0D 3K5MA 3GTQA 2R93A 1A31A 4IP9A 4AHCA 4H3TA 1Y698 3GTJA 1TGOA 3MAQA 1WCMA 3H0GA 1NH3A 3GTOA 3IAYA 2PMZA 1A35A 3FKIA 3K5LA 5JSBB 2A6ED 1RR8C 1SMYD 3LF9A 1EK8A 3K5NA 2B9SB 3LHPS 4EJ3A 4QCLA 1R5ZA 1TWFA 3IGCA 1ISEA 2A69D 1K83A 2H7FX 1WQGA 1YNJD 1SC7A 1HQMD 4NOKA 1EH1A 4F3EA 3KYLA 2YU9A 2H7GX 1IS1A 1A36A 5CQGA 4JLRC 2JA6A 2E2HA 4D3YA 1Q8IA 1SEUA 2BE5D 1I3QA 1I50A 4AN8A 3K5OA 5JSNB 4IP8A
chains in the Genus database with same CATH topology
2JA7A 1WQHA 3P9AA 2R92A 1Y1VA 4O26A 3GTMA 2E2IA 4GFQA 1T8IA 2NVXA 1DD5A 3HKZA 4OYDB 3DU6A 2F4QA 4D3ZA 1WQFA 4C2MA 2R4GA 4NOMA 5MLC9 1V9MA 1TWAA 1VCCA 3WVOA 3M4AA 2O5JD 1Y1WA 4KB4A 2NVYA 4KC6A 4QIWA 1A41A 2WAQA 3CQZA 4L8IA 4LMOA 1YNND 3K57A 4Q5GA 3GTPA 3K59A 2R7ZA 3K58A 1K4SA 3SJRA 4KDDA 4FXDA 2WB1A 4KAWX 2Y0SA 1RRJA 1TWGA 1TL8A 1GE9A 4AYBA 5C9HA 3GTLA 1TWHA 3DU5A 1I6VD 1IW7D 4Q5VA 4FGUA 1SFOA 1R49A 1ZYRD 2A6HD 1EJ9A 1LPQA 2B9SA 1R9TA 2VUMA 2JA5A 2B63A 1TWCA 3GTKA 4FYDA 2A68D 3GTGA 1MIUA 1K4TA 4NOLA 4KB2A 2CW0D 3K5MA 3GTQA 2R93A 1A31A 4IP9A 4AHCA 4H3TA 1Y698 3GTJA 1TGOA 3MAQA 1WCMA 3H0GA 1NH3A 3GTOA 3IAYA 2PMZA 1A35A 3FKIA 3K5LA 5JSBB 2A6ED 1RR8C 1SMYD 3LF9A 1EK8A 3K5NA 2B9SB 3LHPS 4EJ3A 4QCLA 1R5ZA 1TWFA 3IGCA 1ISEA 2A69D 1K83A 2H7FX 1WQGA 1YNJD 1SC7A 1HQMD 4NOKA 1EH1A 4F3EA 3KYLA 2YU9A 2H7GX 1IS1A 1A36A 5CQGA 4JLRC 2JA6A 2E2HA 4D3YA 1Q8IA 1SEUA 2BE5D 1I3QA 1I50A 4AN8A 3K5OA 5JSNB 4IP8A
chains in the Genus database with same CATH homology


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