1RDVA

Rubredoxin from desulfovibrio vulgaris miyazaki f, trigonal crystal form
Total Genus 6
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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
6
sequence length
52
structure length
52
Chain Sequence
b'MKKYVCTVCGYEYDPAEGDPDNGVKPGTAFEDVPADWVCPICGAPKSEFEPA'
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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 RUBREDOXIN
publication title Structure determination of rubredoxin from Desulfovibrio vulgaris Miyazaki F in two crystal forms.
pubmed doi rcsb
molecule tags Electron transfer
total genus 6
structure length 52
sequence length 52
ec nomenclature
pdb deposition date 1998-09-30

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF00301 Rubredoxin Rubredoxin
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
2.20.28.10 Mainly Beta Single Sheet Rubrerythrin, domain 2 Rubrerythrin, domain 2 1rdvA00
1R0HA 4POGA 1BE7A 2PVXA 1FHHA 1DVBA 2M4YA 5AI3A 3RZ6A 3RYGA 1SMUA 3KYVA 4YWLA 2GMGA 1YUZA 1QCVA 1FHMA 1YK4A 1IU6A 2K2DA 1E8JA 1VCXA 4TPUA 1ZRPA 3SS2A 4YWMA 1T9QA 3QVDA 3PZAA 2V3BB 1LKOA 1QYBA 1B71A 1BQ9A 1SMMA 1CADA 1NNQA 1IRNA 3RZTA 3KYXA 1RYTA 3PWFA 1RDGA 1R0JA 1T9PA 1RWDA 2QL0A 2KKDA 1S2ZA 7RXNA 4AR4A 2PYAA 5RXNA 1LKPA 1LTLA 4AR6A 2VL6A 1BQ8A 1C09A 1IU5A 2LCQA 1YK5A 4POFA 1YUXA 3KYWA 1B2JA 1S24A 1H7VA 1JYBA 1B2OA 1S30A 1CAAA 4AR3A 2KN9A 1R0FA 8RXNA 1YV1A 1B13A 2DSXA 4RXNA 1IROA 2PVEA 1RB9A 1LKMA 1BRFA 2HR5A 5IY0A 1RDVA 1T9OA 1BFYA 2RDVA 5AI2A 3KYUA 3MPSA 2MS3A 3KYYA 3A44A 1R0IA 1R0GA 4ME3A 1DX8A 6RXNA 1SMWA 4AR5A 4K9FA
chains in the Genus database with same CATH superfamily
1WCML 2C6BA 2PVXA 3RZ6A 3RYGA 1SMUA 2AQCA 4C3HL 3RZDL 5M3ML 3PIP1 3J7Y1 1WJVA 2K2DA 2B63L 1ZRPA 3PZAA 1I50L 2R93L 1QYBA 1VZHA 2NVTL 1IRNA 3KYXA 3S1RL 1RYTA 3H3VM 4Y52L 2JA6L 4AYBP 2XJSA 2A6ED 3LPEB 5IYDL 1PFUA 2PMZP 5C3EL 2XJQA 3FKIL 1S2ZA 4AR4A 4JAEA 1P7PA 5MGNA 2CKAA 5RXNA 1LTLA 3LWRB 3PO3L 2HVYC 1BQ8A 3GTGL 3S16L 5GADc 4G6BA 1B2JA 4AI2A 1PFVA 1JYBA 4AI1A 2NVXL 3NFPI 4U671 5H1Sc 3H9BA 3H0GL 3LWQB 4A3GL 1B13A 2DSXA 3IU3I 1IROA 2A69D 2PVEA 2V0FA 2Z3RB 4A3ML 3M4OL 1BRFA 3K7AL 1T9OA 2RDVA 3MPSA 3KYYA 3A44A 4AR5A 5K2ME 3PKJA 2NYDA 3GTQL 1FHHA 1TWHL 1DVBA 2M4YA 3M3YL 1TWAL 3WWLA 3B08B 4YWLA 3LNLA 2GMGA 1FHMA 2JI1A 3S14L 1I6HL 2H12A 4ZN3B 5IYBL 1PZXA 1B71A 1BQ9A 1SMMA 2O5JD 1NNQA 5C4JL 2APOB 2E2HL 4C2M1 3PWFA 1R9TL 1RDGA 5C4XL 3HJYB 2RFKB 5M5WL 2KKDA 2PYAA 3K35A 1LKPA 2C6AA 3S1NL 4BBSL 4AR6A 3J7Z1 4QIWP 1C09A 4LHLA 2R7ZL 3I4ML 3KYWA 2PSMC 1S24A 5M5XL 2B5ID 1ODHA 2WB1P 1B2OA 1S30A 2ERJA 1PFWA 1CAAA 3MQKB 2KN9A 1R0FA 8RXNA 3H9CA 2NVYL 2M6OA 3QQCE 2WAQP 3RZOL 3GTOL 1RB9A 3GTPL 4JAFA 1LKMA 2A68D 2HR5A 5IY0A 1NXEA 4A3EL 1RDVA 1R0IA 1R0GA 1VZGA 4A3LL 4XGHA 3S2HL 4A3CL 4WFN1 4A3JL 4AI3A 5IYCL 2XJRA 4POGA 5AI3A 1F4LA 1OWCA 1SFOL 4C3IL 3PIO1 3HOXL 2AUSB 5IP9L 1YK4A 2XJVA 1IU6A 3CQZL 5M5YL 1E8JA 5GAEc 4X6AL 4YWMA 1T9QA 2A6HD 3QVDA 2V3BB 1LKOA 2VUML 4BY7L 3RZTA 4A3KL 4JADA 3I4NL 2XJTA 5IP7L 3GTKL 1T9PA 5MFZA 4JAGA 2XJPA 3GTLL 2JI2A 3GTJL 1Y1VL 1QQTA 3HJWB 1IU5A 3S17L 5AN9H 3HKZP 2LCQA 3S1QL 1I3QL 1YK5A 3S2DL 3PKIA 1H7VA 1PFYA 3H97A 2M6PA 4A3DL 2JI3A 4AHYA 3HAXC 3H99A 2XJUA 3LWVB 5EINC 4A3FL 4RXNA 2R92L 2J9UB 3PL5A 4AHWA 5FJ8L 2E2JL 5GAGc 2M4VA 3KYUA 5DM61 1TWFL 6RXNA 4A93L 4K9FA 3HOVL 1R0HA 2Z3QB 1BE7A 4GS7D 2ERSA 4BY1L 3PO2L 3MSUA 4Y7NL 3LWPB 2YU9L 2JA7L 3GTML 3KYVA 2AYJA 4E6YA 4V196 1YUZA 1QCVA 2CKCA 5FLML 2PPTA 4A3BL 1VCXA 1Y1WL 3ZG6A 4TPUA 3SS2A 2JA8L 2NVQL 5MF6A 3HOUL 1CADA 3FDJA 4AI0A 3P8BA 3S15L 4AHXA 3JR7A 4TVMA 1R0JA 1RWDA 4AHZA 2QL0A 2V0EA 1RYQA 7RXNA 3HOWL 2L0ZA 2VL6A 5EIOC 5M3FL 5JVH1 2JA5L 2CR8A 3P2AA 3HOYL 3WWNB 4LHNA 3HOZL 2BE5D 4POFA 1YUXA 1Z92B 1IW7D 5GAHc 3VPBE 4A3IL 5JVG1 3B0AB 1TWGL 4BBRL 1OWBA 4BXXL 4AR3A 4UY81 1YV1A 4C3JL 4B8CD 2Y0SP 2E2IL 3LWOB 1K83L 1TWCL 4ZN1B 5MFPA 5DM71 2ZIXA 1BFYA 1NXGA 5AI2A 2MS3A 1DX8A 4ME3A 5C44L 1SMWA 1VZIA 5MLC3 3S1ML 2EY4E 4XXBB
chains in the Genus database with same CATH topology
1R0HA 2Z3QB 5K2ME 2XJRA 2NYDA 1BE7A 2C6BA 3PKJA 2ERSA 4GS7D 2PVXA 1FHHA 3MSUA 4POGA 1DVBA 2M4YA 5AI3A 3RZ6A 3WWLA 3RYGA 1SMUA 3B08B 3KYVA 4YWLA 1OWCA 3LNLA 2GMGA 2AYJA 4E6YA 3J7Y1 3PIP1 1WJVA 1YUZA 1QCVA 3PIO1 4V196 1FHMA 2CKCA 1YK4A 2XJVA 1IU6A 2K2DA 2PPTA 2JI1A 1E8JA 1VCXA 3ZG6A 4TPUA 1ZRPA 3SS2A 5GAEc 2H12A 4YWMA 1T9QA 2A6HD 4ZN3B 3PZAA 2V3BB 3QVDA 1LKOA 1QYBA 1VZHA 1B71A 1BQ9A 1SMMA 5MF6A 2O5JD 1CADA 1NNQA 1IRNA 3RZTA 3KYXA 4AI0A 4JADA 3P8BA 1RYTA 4AHXA 2XJTA 3PWFA 1RDGA 2XJSA 2A6ED 4TVMA 1R0JA 1T9PA 3LPEB 1RWDA 5MFZA 4AR5A 4AHZA 2QL0A 2V0EA 2XJPA 4JAGA 2XJQA 1RYQA 2KKDA 1S2ZA 2JI2A 7RXNA 4AR4A 2PYAA 4JAEA 3K35A 5MGNA 2CKAA 5RXNA 1LKPA 2C6AA 2L0ZA 1LTLA 4AR6A 2VL6A 5EIOC 3J7Z1 5JVH1 1BQ8A 1C09A 2CR8A 3P2AA 1IU5A 5AN9H 4LHLA 2LCQA 3WWNB 1YK5A 4LHNA 5GADc 2BE5D 4POFA 4G6BA 1YUXA 3KYWA 1B2JA 2PSMC 4AI2A 3PKIA 1S24A 1Z92B 1IW7D 5GAHc 3VPBE 1H7VA 5JVG1 1JYBA 3B0AB 2B5ID 2M6PA 2JI3A 4AI1A 4AHYA 1ODHA 1B2OA 1OWBA 1S30A 3NFPI 2ERJA 1CAAA 4U671 4AR3A 2KN9A 1R0FA 2XJUA 5H1Sc 8RXNA 4UY81 1YV1A 2M6OA 5EINC 1B13A 4B8CD 3QQCE 2DSXA 4RXNA 4XXBB 3IU3I 1IROA 2A69D 2PVEA 1RB9A 2V0FA 2Z3RB 4JAFA 4ZN1B 1LKMA 2J9UB 2A68D 4AHWA 5MFPA 1BRFA 2HR5A 5DM71 5IY0A 1NXEA 1RDVA 2ZIXA 1T9OA 1BFYA 5GAGc 1NXGA 2RDVA 5AI2A 2M4VA 3KYUA 2MS3A 3KYYA 3A44A 3MPSA 1R0IA 4ME3A 1R0GA 5DM61 1DX8A 1VZGA 6RXNA 1SMWA 1VZIA 4XGHA 5MLC3 4WFN1 4AI3A 4K9FA
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 1R0H A;  4POG A;  1BE7 A;  2PVX A;  1FHH A;  1DVB A;  2M4Y A;  5AI3 A;  3RZ6 A;  3RYG A;  1SMU A;  3KYV A;  4YWL A;  2GMG A;  1YUZ A;  1QCV A;  1FHM A;  1YK4 A;  1IU6 A;  2K2D A;  1E8J A;  1VCX A;  4TPU A;  1ZRP A;  3SS2 A;  4YWM A;  1T9Q A;  3QVD A;  3PZA A;  2V3B B;  1LKO A;  1QYB A;  1B71 A;  1BQ9 A;  1SMM A;  1CAD A;  1NNQ A;  1IRN A;  3RZT A;  3KYX A;  1RYT A;  3PWF A;  1RDG A;  1R0J A;  1T9P A;  1RWD A;  2QL0 A;  2KKD A;  1S2Z A;  7RXN A;  4AR4 A;  2PYA A;  5RXN A;  1LKP A;  1LTL A;  4AR6 A;  2VL6 A;  1BQ8 A;  1C09 A;  1IU5 A;  2LCQ A;  1YK5 A;  4POF A;  1YUX A;  3KYW A;  1B2J A;  1S24 A;  1H7V A;  1JYB A;  1B2O A;  1S30 A;  1CAA A;  4AR3 A;  2KN9 A;  1R0F A;  8RXN A;  1YV1 A;  1B13 A;  2DSX A;  4RXN A;  1IRO A;  2PVE A;  1RB9 A;  1LKM A;  1BRF A;  2HR5 A;  5IY0 A;  1RDV A;  1T9O A;  1BFY A;  2RDV A;  5AI2 A;  3KYU A;  3MPS A;  2MS3 A;  3KYY A;  3A44 A;  1R0I A;  1R0G A;  4ME3 A;  1DX8 A;  6RXN A;  1SMW A;  4AR5 A;  4K9F A; 
#chains in the Genus database with same CATH topology
 1WCM L;  2C6B A;  2PVX A;  3RZ6 A;  3RYG A;  1SMU A;  2AQC A;  4C3H L;  3RZD L;  5M3M L;  3PIP 1;  3J7Y 1;  1WJV A;  2K2D A;  2B63 L;  1ZRP A;  3PZA A;  1I50 L;  2R93 L;  1QYB A;  1VZH A;  2NVT L;  1IRN A;  3KYX A;  3S1R L;  1RYT A;  3H3V M;  4Y52 L;  2JA6 L;  4AYB P;  2XJS A;  2A6E D;  3LPE B;  5IYD L;  1PFU A;  2PMZ P;  5C3E L;  2XJQ A;  3FKI L;  1S2Z A;  4AR4 A;  4JAE A;  1P7P A;  5MGN A;  2CKA A;  5RXN A;  1LTL A;  3LWR B;  3PO3 L;  2HVY C;  1BQ8 A;  3GTG L;  3S16 L;  5GAD c;  4G6B A;  1B2J A;  4AI2 A;  1PFV A;  1JYB A;  4AI1 A;  2NVX L;  3NFP I;  4U67 1;  5H1S c;  3H9B A;  3H0G L;  3LWQ B;  4A3G L;  1B13 A;  2DSX A;  3IU3 I;  1IRO A;  2A69 D;  2PVE A;  2V0F A;  2Z3R B;  4A3M L;  3M4O L;  1BRF A;  3K7A L;  1T9O A;  2RDV A;  3MPS A;  3KYY A;  3A44 A;  4AR5 A;  5K2M E;  3PKJ A;  2NYD A;  3GTQ L;  1FHH A;  1TWH L;  1DVB A;  2M4Y A;  3M3Y L;  1TWA L;  3WWL A;  3B08 B;  4YWL A;  3LNL A;  2GMG A;  1FHM A;  2JI1 A;  3S14 L;  1I6H L;  2H12 A;  4ZN3 B;  5IYB L;  1PZX A;  1B71 A;  1BQ9 A;  1SMM A;  2O5J D;  1NNQ A;  5C4J L;  2APO B;  2E2H L;  4C2M 1;  3PWF A;  1R9T L;  1RDG A;  5C4X L;  3HJY B;  2RFK B;  5M5W L;  2KKD A;  2PYA A;  3K35 A;  1LKP A;  2C6A A;  3S1N L;  4BBS L;  4AR6 A;  3J7Z 1;  4QIW P;  1C09 A;  4LHL A;  2R7Z L;  3I4M L;  3KYW A;  2PSM C;  1S24 A;  5M5X L;  2B5I D;  1ODH A;  2WB1 P;  1B2O A;  1S30 A;  2ERJ A;  1PFW A;  1CAA A;  3MQK B;  2KN9 A;  1R0F A;  8RXN A;  3H9C A;  2NVY L;  2M6O A;  3QQC E;  2WAQ P;  3RZO L;  3GTO L;  1RB9 A;  3GTP L;  4JAF A;  1LKM A;  2A68 D;  2HR5 A;  5IY0 A;  1NXE A;  4A3E L;  1RDV A;  1R0I A;  1R0G A;  1VZG A;  4A3L L;  4XGH A;  3S2H L;  4A3C L;  4WFN 1;  4A3J L;  4AI3 A;  5IYC L;  2XJR A;  4POG A;  5AI3 A;  1F4L A;  1OWC A;  1SFO L;  4C3I L;  3PIO 1;  3HOX L;  2AUS B;  5IP9 L;  1YK4 A;  2XJV A;  1IU6 A;  3CQZ L;  5M5Y L;  1E8J A;  5GAE c;  4X6A L;  4YWM A;  1T9Q A;  2A6H D;  3QVD A;  2V3B B;  1LKO A;  2VUM L;  4BY7 L;  3RZT A;  4A3K L;  4JAD A;  3I4N L;  2XJT A;  5IP7 L;  3GTK L;  1T9P A;  5MFZ A;  4JAG A;  2XJP A;  3GTL L;  2JI2 A;  3GTJ L;  1Y1V L;  1QQT A;  3HJW B;  1IU5 A;  3S17 L;  5AN9 H;  3HKZ P;  2LCQ A;  3S1Q L;  1I3Q L;  1YK5 A;  3S2D L;  3PKI A;  1H7V A;  1PFY A;  3H97 A;  2M6P A;  4A3D L;  2JI3 A;  4AHY A;  3HAX C;  3H99 A;  2XJU A;  3LWV B;  5EIN C;  4A3F L;  4RXN A;  2R92 L;  2J9U B;  3PL5 A;  4AHW A;  5FJ8 L;  2E2J L;  5GAG c;  2M4V A;  3KYU A;  5DM6 1;  1TWF L;  6RXN A;  4A93 L;  4K9F A;  3HOV L;  1R0H A;  2Z3Q B;  1BE7 A;  4GS7 D;  2ERS A;  4BY1 L;  3PO2 L;  3MSU A;  4Y7N L;  3LWP B;  2YU9 L;  2JA7 L;  3GTM L;  3KYV A;  2AYJ A;  4E6Y A;  4V19 6;  1YUZ A;  1QCV A;  2CKC A;  5FLM L;  2PPT A;  4A3B L;  1VCX A;  1Y1W L;  3ZG6 A;  4TPU A;  3SS2 A;  2JA8 L;  2NVQ L;  5MF6 A;  3HOU L;  1CAD A;  3FDJ A;  4AI0 A;  3P8B A;  3S15 L;  4AHX A;  3JR7 A;  4TVM A;  1R0J A;  1RWD A;  4AHZ A;  2QL0 A;  2V0E A;  1RYQ A;  7RXN A;  3HOW L;  2L0Z A;  2VL6 A;  5EIO C;  5M3F L;  5JVH 1;  2JA5 L;  2CR8 A;  3P2A A;  3HOY L;  3WWN B;  4LHN A;  3HOZ L;  2BE5 D;  4POF A;  1YUX A;  1Z92 B;  1IW7 D;  5GAH c;  3VPB E;  4A3I L;  5JVG 1;  3B0A B;  1TWG L;  4BBR L;  1OWB A;  4BXX L;  4AR3 A;  4UY8 1;  1YV1 A;  4C3J L;  4B8C D;  2Y0S P;  2E2I L;  3LWO B;  1K83 L;  1TWC L;  4ZN1 B;  5MFP A;  5DM7 1;  2ZIX A;  1BFY A;  1NXG A;  5AI2 A;  2MS3 A;  1DX8 A;  4ME3 A;  5C44 L;  1SMW A;  1VZI A;  5MLC 3;  3S1M L;  2EY4 E;  4XXB B; 
#chains in the Genus database with same CATH homology
 1R0H A;  2Z3Q B;  5K2M E;  2XJR A;  2NYD A;  1BE7 A;  2C6B A;  3PKJ A;  2ERS A;  4GS7 D;  2PVX A;  1FHH A;  3MSU A;  4POG A;  1DVB A;  2M4Y A;  5AI3 A;  3RZ6 A;  3WWL A;  3RYG A;  1SMU A;  3B08 B;  3KYV A;  4YWL A;  1OWC A;  3LNL A;  2GMG A;  2AYJ A;  4E6Y A;  3J7Y 1;  3PIP 1;  1WJV A;  1YUZ A;  1QCV A;  3PIO 1;  4V19 6;  1FHM A;  2CKC A;  1YK4 A;  2XJV A;  1IU6 A;  2K2D A;  2PPT A;  2JI1 A;  1E8J A;  1VCX A;  3ZG6 A;  4TPU A;  1ZRP A;  3SS2 A;  5GAE c;  2H12 A;  4YWM A;  1T9Q A;  2A6H D;  4ZN3 B;  3PZA A;  2V3B B;  3QVD A;  1LKO A;  1QYB A;  1VZH A;  1B71 A;  1BQ9 A;  1SMM A;  5MF6 A;  2O5J D;  1CAD A;  1NNQ A;  1IRN A;  3RZT A;  3KYX A;  4AI0 A;  4JAD A;  3P8B A;  1RYT A;  4AHX A;  2XJT A;  3PWF A;  1RDG A;  2XJS A;  2A6E D;  4TVM A;  1R0J A;  1T9P A;  3LPE B;  1RWD A;  5MFZ A;  4AR5 A;  4AHZ A;  2QL0 A;  2V0E A;  2XJP A;  4JAG A;  2XJQ A;  1RYQ A;  2KKD A;  1S2Z A;  2JI2 A;  7RXN A;  4AR4 A;  2PYA A;  4JAE A;  3K35 A;  5MGN A;  2CKA A;  5RXN A;  1LKP A;  2C6A A;  2L0Z A;  1LTL A;  4AR6 A;  2VL6 A;  5EIO C;  3J7Z 1;  5JVH 1;  1BQ8 A;  1C09 A;  2CR8 A;  3P2A A;  1IU5 A;  5AN9 H;  4LHL A;  2LCQ A;  3WWN B;  1YK5 A;  4LHN A;  5GAD c;  2BE5 D;  4POF A;  4G6B A;  1YUX A;  3KYW A;  1B2J A;  2PSM C;  4AI2 A;  3PKI A;  1S24 A;  1Z92 B;  1IW7 D;  5GAH c;  3VPB E;  1H7V A;  5JVG 1;  1JYB A;  3B0A B;  2B5I D;  2M6P A;  2JI3 A;  4AI1 A;  4AHY A;  1ODH A;  1B2O A;  1OWB A;  1S30 A;  3NFP I;  2ERJ A;  1CAA A;  4U67 1;  4AR3 A;  2KN9 A;  1R0F A;  2XJU A;  5H1S c;  8RXN A;  4UY8 1;  1YV1 A;  2M6O A;  5EIN C;  1B13 A;  4B8C D;  3QQC E;  2DSX A;  4RXN A;  4XXB B;  3IU3 I;  1IRO A;  2A69 D;  2PVE A;  1RB9 A;  2V0F A;  2Z3R B;  4JAF A;  4ZN1 B;  1LKM A;  2J9U B;  2A68 D;  4AHW A;  5MFP A;  1BRF A;  2HR5 A;  5DM7 1;  5IY0 A;  1NXE A;  1RDV A;  2ZIX A;  1T9O A;  1BFY A;  5GAG c;  1NXG A;  2RDV A;  5AI2 A;  2M4V A;  3KYU A;  2MS3 A;  3KYY A;  3A44 A;  3MPS A;  1R0I A;  4ME3 A;  1R0G A;  5DM6 1;  1DX8 A;  1VZG A;  6RXN A;  1SMW A;  1VZI A;  4XGH A;  5MLC 3;  4WFN 1;  4AI3 A;  4K9F 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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