3H3V | Genus

Total Genus 43

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	43
sequence length	218
structure length	177
Chain Sequence	STSTFQTRRRRLKKVEEEENAATLQLGQEFQLKQINHQGEEEELIALNLSEARLVIKEALVERRRAFKRSQKKTREKELESIDVLLEQTTGGNNKDLKNTMQYLTNFSRFRDQETVGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLNNKISDDELERILKELSNLETLY

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

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The Resolver thinks Pdb

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Time for openFile(/file/5d2641d685b01f4dc6ebd1f5/pdb.gz): 1259 ms

reading 177 atoms

ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false

1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.

Default Van der Waals type for model set to Jmol

177 atoms created

ModelSet: autobonding; use autobond=false to not generate bonds automatically

Time for creating model: 22 ms

Adding embedded #jmolscript: select ({0:176});backbone only;select *;

After clicking on a point (x,y) in the genus matrix above, a subchain from x to y is shown in color.

Genus data interpretation

Chord Diagram

molecule tags	Transferase/dna/rna
publication title	Torpedo Nuclease Rat1 Is Insufficient to Terminate RNA Polymerase II in Vitro pubmed doi rcsb
molecule keywords	DNA-directed RNA polymerase II subunit RPB1
total genus	43
structure length	177
sequence length	218
ec nomenclature
pdb deposition date	2009-04-17

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
E	PF03874	RNA_pol_Rpb4	RNA polymerase Rpb4

Image from the rcsb pdb (www.rcsb.org)

cath code	Class	Architecture	Topology	Homology	Domain
1.20.1250.40	Mainly Alpha	Up-down Bundle	Growth Hormone; Chain: A;	Growth Hormone; Chain: A;	3h3vE02

5C3ED 3HOWD 3H3VE 3HOYD 3I4ND 4A3ID 3HOUD 4A3MD 5IYDD 2C35A 4A93D 2VUMD 2R92D 4A3BD 4A3KD 2JA5D 2JA6D 4BY7D 3HOVD 4A3FD 3H0GD 2B63D 3PO3D 3HOXD 4A3ED 4A3DD 3PO2D 4A3LD 3FKID 4BY1D 5IYBD 3HOZD 4A3CD 4BBSD 1Y1WD 3I4MD 2R93D 5IP7D 4BXXD 5IP9D 2JA7D 2R7ZD 1WCMD 3AYHA 5IYCD 5C4XD 2JA8D 4BBRD 5C44D 1Y14A 4A3GD 5FLMD 1Y1VD 4A3JD
chains in the Genus database with same CATH superfamily

4EXNA 4ZYRA 3I4ND 4J05A 1RFBA 2INTA 4YQXA 3HHCA 4NI7A 1ITMA 4A3LD 2Q98A 4YPGC 5IP7D 4IKYA 2PSMA 4O6KA 3NPZA 4DKEA 1CD9A 3DGCL 2XUTA 3UEZE 3BESL 1EKUA 4A3BD 4D2DA 4D2BA 2O27A 3QAZA 4NKQC 5IYBD 4NN5A 1BCNA 1VLKA 1BGCA 2R7ZD 3LB6B 1KF9A 4I77Z 1HWGA 4A3GD 1Z92A 2B91A 4WRLB 5FLMD 4PS4A 4A3MD 4A93D 2GMFA 3VA2A 3O7PA 2L3YA 3SE3B 2JA5D 4XNIA 3PO3D 2H24A 1RHGA 1Y1WD 2Z3RA 4BXXD 5IP9D 2JA7D 2O26A 5C44D 4ZS7A 2B8YA 5FUCA 3QB1A 3PIWA 2Z3QA 5FHXA 5KNHI 1B5LA 3NCFA 1BUYA 4YUEC 4JREA 1V7MV 4Q65A 3OG4A 3DI3A 2B63D 2ERJD 3PO2D 1WU3I 4ZW9A 1PW4A 4RS1A 2HYMB 3UX9A 3INKC 5C4XD 1D9CA 1LQSL 1M49A 4NEMA 5D22A 5GXBA 4UVMA 5D71A 2CFQA 3OG6A 5D28B 1M47A 4W6VA 1V7NV 4XNJA 4BBRD 3HOWD 4O9HA 1YKBA 4ZF7A 1HULA 1GA3A 3HOXD 3HOZD 4GBYA 1EMRA 3UF2A 4EXPA 2B8XA 1P9MB 4YBQA 1WCMD 1GNCA 2CYKA 4JR9A 2L3OA 5C3ED 3DUHC 4NN6A 4ZWBA 1F6FA 3G9VB 3DLQI 2JA6D 1Z7CA 4IKZA 3EW3A 1HIJA 2Q7NB 3AYHA 3D85C 2JA8D 1HZIA 1JLIA 2Y5YA 1EERA 1FG9A 1Y6NL 1IJZA 1CYLA 2CFPA 4BY7D 2E9WC 4YB9D 3DI2A 4BBSD 4DKDA 3I4MD 2O6IA 4TPGA 1HIKA 2R93D 5EQHA 3NCBA 1CN4C 1M48A 2LMSA 1NBPA 4DKFA 3BPOA 4TPJA 1BGEA 3G6DA 3D48P 2LAGA 5D70A 4FA8E 4IKXA 1PGRA 3PIVA 1EXZA 4U4VA 1AXIA 1HUWA 3Q1SI 1IL6A 1N1FA 1I1RB 3L5XA 1A22A 4IKVA 3FKID 4GBZA 3N06A 5A2NA 5IYCD 1BGDA 1ITFA 1PY2A 1M4RA 1LKIA 4A3ID 3HOUD 4OH3A 4NN7A 2B90A 4X51A 5C7XA 4PYPA 1QVNA 4IU8A 5L6YC 1RW5A 1FYHA 4DKCA 1LK3A 5LQBA 3QT2C 4J4LC 4NEJA 2D48A 1RCBA 5D59A 4NI9A 3OQ3A 2B8ZA 4BY1D 1Y6KL 3SE4B 3BPLA 5A2OA 4GRWA 3HHRA 4CNIC 3QB7A 1Y14A 3HMXB 4A3JD 1IRLA 2V8NA 3L5WI 1INRA 2R92D 1ALUA 3HOVD 3B5KA 3BPNA 2B5IA 4A3CD 4U4TA 3O7QA 4IU9A 1M4AA 4LDSA 1BBNA 3HOYD 5TS9A 3N0PA 2VUMD 1D9GA 4QIQA 3NCEA 4OAAA 1AU1A 1AX8A 3NCCA 3H0GD 4A3FD 4LEPA 1CNT1 5E4EA 4DOHA 3LB6A 1M4BA 2Q14A 3EJJA 2IL6A 1Y1VD 1PV7A 4MHLA 1ILKA 3MZGA 3IRHA 4LRLA 1PW6A 3WCYI 1SCFA 4ZWCA 1BP3A 4A3DD 4GS7A 1PV6A 5D6KA 1F45B 3UF5A 5EQIA 1HGUA 4JA3A 4IKWA 4GC0A 4Z5RD 3H3VE 4U4WA 5IYDD 1HWHA 2C35A 2B8UA 2ILKA 5EQGA 1EVSA 3QWRB 1IK0A 1ITIA 3D87A 1ETEA 5C65A 1ITLA 4APSA 2OQPA 3S9DA 1CSGA 4YDYI 2XQBA 4A3KD 1PVHB 4D2CA 1Y6ML 4A3ED 1A7MA 2KZ1A 5D58A 3TGXB 3WDOA 5D72A 4TPHA 1M4CA 2D9QA 1IARA 1J7VL
chains in the Genus database with same CATH topology

1D9CA 3BPOA 1M4AA 4EXNA 1BGEA 1LQSL 3G6DA 1BBNA 3D48P 3HOYD 2LAGA 3I4ND 1M49A 1RFBA 4NEMA 5D70A 5TS9A 4FA8E 5D22A 3N0PA 2INTA 2VUMD 1D9GA 1PGRA 3PIVA 1EXZA 3NCEA 1AU1A 1AXIA 4YQXA 1AX8A 1HUWA 3NCCA 3H0GD 3Q1SI 1IL6A 1CNT1 3HHCA 1N1FA 1I1RB 3L5XA 1ITMA 4NI7A 1A22A 5E4EA 4DOHA 4A3LD 3FKID 3LB6A 1M4BA 2Q14A 5D71A 2Q98A 4A3FD 3N06A 3EJJA 2IL6A 3OG6A 4YPGC 5IP7D 5D28B 1M47A 1V7NV 2PSMA 4O6KA 5IYCD 4BBRD 3NPZA 4DKEA 1Y1VD 1BGDA 3HOWD 1ITFA 1CD9A 4O9HA 3DGCL 1PY2A 1M4RA 1YKBA 4MHLA 1LKIA 4A3ID 3UEZE 3HOUD 1ILKA 3MZGA 4NN7A 3BESL 3IRHA 2B90A 4LRLA 4X51A 4ZF7A 1EKUA 1PW6A 3WCYI 1HULA 4A3BD 5C7XA 1SCFA 1GA3A 2O27A 1QVNA 3QAZA 1BP3A 3HOXD 4A3DD 4NKQC 4GS7A 5L6YC 5IYBD 3HOZD 4NN5A 1EMRA 3UF2A 4EXPA 1RW5A 1F45B 3UF5A 1BCNA 1VLKA 1BGCA 2B8XA 1HGUA 1P9MB 2R7ZD 1FYHA 1WCMD 1GNCA 3LB6B 1KF9A 2CYKA 1HWGA 4I77Z 2L3OA 4A3GD 1Z92A 2B91A 4WRLB 5FLMD 4DKCA 1LK3A 4PS4A 3DUHC 5C3ED 4Z5RD 3H3VE 5LQBA 3QT2C 4NN6A 5IYDD 4A3MD 1F6FA 1HWHA 2C35A 4J4LC 4NEJA 3G9VB 2GMFA 4A93D 3DLQI 2D48A 3VA2A 2B8UA 2ILKA 2L3YA 1EVSA 3QWRB 3SE3B 2JA5D 1Z7CA 2JA6D 1IK0A 1RCBA 1ITIA 4NI9A 3OQ3A 3EW3A 3PO3D 2H24A 2B8ZA 1HIJA 4BY1D 1RHGA 1Y6KL 3SE4B 3BPLA 1Y1WD 2Q7NB 3D87A 1ETEA 2Z3RA 4GRWA 3HHRA 4BXXD 4CNIC 5IP9D 3QB7A 2JA7D 1ITLA 2OQPA 3AYHA 3S9DA 1CSGA 2O26A 3D85C 2JA8D 5C44D 1Y14A 3HMXB 4YDYI 4A3JD 1IRLA 1HZIA 1JLIA 4ZS7A 2B8YA 1EERA 3L5WI 1INRA 5FUCA 1FG9A 2XQBA 3QB1A 1Y6NL 1IJZA 3PIWA 2Z3QA 1CYLA 2R92D 5FHXA 5KNHI 1ALUA 1B5LA 4A3KD 3NCFA 1BUYA 4YUEC 4BY7D 3HOVD 1V7MV 1PVHB 2E9WC 3DI3A 3OG4A 2B63D 2ERJD 1Y6ML 3B5KA 3BPNA 4A3ED 3PO2D 1A7MA 2B5IA 2KZ1A 3DI2A 4A3CD 4BBSD 4DKDA 3TGXB 1WU3I 2O6IA 3I4MD 5D72A 1HIKA 4RS1A 2R93D 2HYMB 3NCBA 1CN4C 1M48A 1M4CA 2LMSA 3UX9A 1NBPA 2D9QA 3INKC 1IARA 5C4XD 4DKFA 1J7VL
chains in the Genus database with same CATH homology

#chains in the Genus database with same CATH superfamily
 5C3E D;  3HOW D;  3H3V E;  3HOY D;  3I4N D;  4A3I D;  3HOU D;  4A3M D;  5IYD D;  2C35 A;  4A93 D;  2VUM D;  2R92 D;  4A3B D;  4A3K D;  2JA5 D;  2JA6 D;  4BY7 D;  3HOV D;  4A3F D;  3H0G D;  2B63 D;  3PO3 D;  3HOX D;  4A3E D;  4A3D D;  3PO2 D;  4A3L D;  3FKI D;  4BY1 D;  5IYB D;  3HOZ D;  4A3C D;  4BBS D;  1Y1W D;  3I4M D;  2R93 D;  5IP7 D;  4BXX D;  5IP9 D;  2JA7 D;  2R7Z D;  1WCM D;  3AYH A;  5IYC D;  5C4X D;  2JA8 D;  4BBR D;  5C44 D;  1Y14 A;  4A3G D;  5FLM D;  1Y1V D;  4A3J D; 
#chains in the Genus database with same CATH topology
 4EXN A;  4ZYR A;  3I4N D;  4J05 A;  1RFB A;  2INT A;  4YQX A;  3HHC A;  4NI7 A;  1ITM A;  4A3L D;  2Q98 A;  4YPG C;  5IP7 D;  4IKY A;  2PSM A;  4O6K A;  3NPZ A;  4DKE A;  1CD9 A;  3DGC L;  2XUT A;  3UEZ E;  3BES L;  1EKU A;  4A3B D;  4D2D A;  4D2B A;  2O27 A;  3QAZ A;  4NKQ C;  5IYB D;  4NN5 A;  1BCN A;  1VLK A;  1BGC A;  2R7Z D;  3LB6 B;  1KF9 A;  4I77 Z;  1HWG A;  4A3G D;  1Z92 A;  2B91 A;  4WRL B;  5FLM D;  4PS4 A;  4A3M D;  4A93 D;  2GMF A;  3VA2 A;  3O7P A;  2L3Y A;  3SE3 B;  2JA5 D;  4XNI A;  3PO3 D;  2H24 A;  1RHG A;  1Y1W D;  2Z3R A;  4BXX D;  5IP9 D;  2JA7 D;  2O26 A;  5C44 D;  4ZS7 A;  2B8Y A;  5FUC A;  3QB1 A;  3PIW A;  2Z3Q A;  5FHX A;  5KNH I;  1B5L A;  3NCF A;  1BUY A;  4YUE C;  4JRE A;  1V7M V;  4Q65 A;  3OG4 A;  3DI3 A;  2B63 D;  2ERJ D;  3PO2 D;  1WU3 I;  4ZW9 A;  1PW4 A;  4RS1 A;  2HYM B;  3UX9 A;  3INK C;  5C4X D;  1D9C A;  1LQS L;  1M49 A;  4NEM A;  5D22 A;  5GXB A;  4UVM A;  5D71 A;  2CFQ A;  3OG6 A;  5D28 B;  1M47 A;  4W6V A;  1V7N V;  4XNJ A;  4BBR D;  3HOW D;  4O9H A;  1YKB A;  4ZF7 A;  1HUL A;  1GA3 A;  3HOX D;  3HOZ D;  4GBY A;  1EMR A;  3UF2 A;  4EXP A;  2B8X A;  1P9M B;  4YBQ A;  1WCM D;  1GNC A;  2CYK A;  4JR9 A;  2L3O A;  5C3E D;  3DUH C;  4NN6 A;  4ZWB A;  1F6F A;  3G9V B;  3DLQ I;  2JA6 D;  1Z7C A;  4IKZ A;  3EW3 A;  1HIJ A;  2Q7N B;  3AYH A;  3D85 C;  2JA8 D;  1HZI A;  1JLI A;  2Y5Y A;  1EER A;  1FG9 A;  1Y6N L;  1IJZ A;  1CYL A;  2CFP A;  4BY7 D;  2E9W C;  4YB9 D;  3DI2 A;  4BBS D;  4DKD A;  3I4M D;  2O6I A;  4TPG A;  1HIK A;  2R93 D;  5EQH A;  3NCB A;  1CN4 C;  1M48 A;  2LMS A;  1NBP A;  4DKF A;  3BPO A;  4TPJ A;  1BGE A;  3G6D A;  3D48 P;  2LAG A;  5D70 A;  4FA8 E;  4IKX A;  1PGR A;  3PIV A;  1EXZ A;  4U4V A;  1AXI A;  1HUW A;  3Q1S I;  1IL6 A;  1N1F A;  1I1R B;  3L5X A;  1A22 A;  4IKV A;  3FKI D;  4GBZ A;  3N06 A;  5A2N A;  5IYC D;  1BGD A;  1ITF A;  1PY2 A;  1M4R A;  1LKI A;  4A3I D;  3HOU D;  4OH3 A;  4NN7 A;  2B90 A;  4X51 A;  5C7X A;  4PYP A;  1QVN A;  4IU8 A;  5L6Y C;  1RW5 A;  1FYH A;  4DKC A;  1LK3 A;  5LQB A;  3QT2 C;  4J4L C;  4NEJ A;  2D48 A;  1RCB A;  5D59 A;  4NI9 A;  3OQ3 A;  2B8Z A;  4BY1 D;  1Y6K L;  3SE4 B;  3BPL A;  5A2O A;  4GRW A;  3HHR A;  4CNI C;  3QB7 A;  1Y14 A;  3HMX B;  4A3J D;  1IRL A;  2V8N A;  3L5W I;  1INR A;  2R92 D;  1ALU A;  3HOV D;  3B5K A;  3BPN A;  2B5I A;  4A3C D;  4U4T A;  3O7Q A;  4IU9 A;  1M4A A;  4LDS A;  1BBN A;  3HOY D;  5TS9 A;  3N0P A;  2VUM D;  1D9G A;  4QIQ A;  3NCE A;  4OAA A;  1AU1 A;  1AX8 A;  3NCC A;  3H0G D;  4A3F D;  4LEP A;  1CNT 1;  5E4E A;  4DOH A;  3LB6 A;  1M4B A;  2Q14 A;  3EJJ A;  2IL6 A;  1Y1V D;  1PV7 A;  4MHL A;  1ILK A;  3MZG A;  3IRH A;  4LRL A;  1PW6 A;  3WCY I;  1SCF A;  4ZWC A;  1BP3 A;  4A3D D;  4GS7 A;  1PV6 A;  5D6K A;  1F45 B;  3UF5 A;  5EQI A;  1HGU A;  4JA3 A;  4IKW A;  4GC0 A;  4Z5R D;  3H3V E;  4U4W A;  5IYD D;  1HWH A;  2C35 A;  2B8U A;  2ILK A;  5EQG A;  1EVS A;  3QWR B;  1IK0 A;  1ITI A;  3D87 A;  1ETE A;  5C65 A;  1ITL A;  4APS A;  2OQP A;  3S9D A;  1CSG A;  4YDY I;  2XQB A;  4A3K D;  1PVH B;  4D2C A;  1Y6M L;  4A3E D;  1A7M A;  2KZ1 A;  5D58 A;  3TGX B;  3WDO A;  5D72 A;  4TPH A;  1M4C A;  2D9Q A;  1IAR A;  1J7V L; 
#chains in the Genus database with same CATH homology
 1D9C A;  3BPO A;  1M4A A;  4EXN A;  1BGE A;  1LQS L;  3G6D A;  1BBN A;  3D48 P;  3HOY D;  2LAG A;  3I4N D;  1M49 A;  1RFB A;  4NEM A;  5D70 A;  5TS9 A;  4FA8 E;  5D22 A;  3N0P A;  2INT A;  2VUM D;  1D9G A;  1PGR A;  3PIV A;  1EXZ A;  3NCE A;  1AU1 A;  1AXI A;  4YQX A;  1AX8 A;  1HUW A;  3NCC A;  3H0G D;  3Q1S I;  1IL6 A;  1CNT 1;  3HHC A;  1N1F A;  1I1R B;  3L5X A;  1ITM A;  4NI7 A;  1A22 A;  5E4E A;  4DOH A;  4A3L D;  3FKI D;  3LB6 A;  1M4B A;  2Q14 A;  5D71 A;  2Q98 A;  4A3F D;  3N06 A;  3EJJ A;  2IL6 A;  3OG6 A;  4YPG C;  5IP7 D;  5D28 B;  1M47 A;  1V7N V;  2PSM A;  4O6K A;  5IYC D;  4BBR D;  3NPZ A;  4DKE A;  1Y1V D;  1BGD A;  3HOW D;  1ITF A;  1CD9 A;  4O9H A;  3DGC L;  1PY2 A;  1M4R A;  1YKB A;  4MHL A;  1LKI A;  4A3I D;  3UEZ E;  3HOU D;  1ILK A;  3MZG A;  4NN7 A;  3BES L;  3IRH A;  2B90 A;  4LRL A;  4X51 A;  4ZF7 A;  1EKU A;  1PW6 A;  3WCY I;  1HUL A;  4A3B D;  5C7X A;  1SCF A;  1GA3 A;  2O27 A;  1QVN A;  3QAZ A;  1BP3 A;  3HOX D;  4A3D D;  4NKQ C;  4GS7 A;  5L6Y C;  5IYB D;  3HOZ D;  4NN5 A;  1EMR A;  3UF2 A;  4EXP A;  1RW5 A;  1F45 B;  3UF5 A;  1BCN A;  1VLK A;  1BGC A;  2B8X A;  1HGU A;  1P9M B;  2R7Z D;  1FYH A;  1WCM D;  1GNC A;  3LB6 B;  1KF9 A;  2CYK A;  1HWG A;  4I77 Z;  2L3O A;  4A3G D;  1Z92 A;  2B91 A;  4WRL B;  5FLM D;  4DKC A;  1LK3 A;  4PS4 A;  3DUH C;  5C3E D;  4Z5R D;  3H3V E;  5LQB A;  3QT2 C;  4NN6 A;  5IYD D;  4A3M D;  1F6F A;  1HWH A;  2C35 A;  4J4L C;  4NEJ A;  3G9V B;  2GMF A;  4A93 D;  3DLQ I;  2D48 A;  3VA2 A;  2B8U A;  2ILK A;  2L3Y A;  1EVS A;  3QWR B;  3SE3 B;  2JA5 D;  1Z7C A;  2JA6 D;  1IK0 A;  1RCB A;  1ITI A;  4NI9 A;  3OQ3 A;  3EW3 A;  3PO3 D;  2H24 A;  2B8Z A;  1HIJ A;  4BY1 D;  1RHG A;  1Y6K L;  3SE4 B;  3BPL A;  1Y1W D;  2Q7N B;  3D87 A;  1ETE A;  2Z3R A;  4GRW A;  3HHR A;  4BXX D;  4CNI C;  5IP9 D;  3QB7 A;  2JA7 D;  1ITL A;  2OQP A;  3AYH A;  3S9D A;  1CSG A;  2O26 A;  3D85 C;  2JA8 D;  5C44 D;  1Y14 A;  3HMX B;  4YDY I;  4A3J D;  1IRL A;  1HZI A;  1JLI A;  4ZS7 A;  2B8Y A;  1EER A;  3L5W I;  1INR A;  5FUC A;  1FG9 A;  2XQB A;  3QB1 A;  1Y6N L;  1IJZ A;  3PIW A;  2Z3Q A;  1CYL A;  2R92 D;  5FHX A;  5KNH I;  1ALU A;  1B5L A;  4A3K D;  3NCF A;  1BUY A;  4YUE C;  4BY7 D;  3HOV D;  1V7M V;  1PVH B;  2E9W C;  3DI3 A;  3OG4 A;  2B63 D;  2ERJ D;  1Y6M L;  3B5K A;  3BPN A;  4A3E D;  3PO2 D;  1A7M A;  2B5I A;  2KZ1 A;  3DI2 A;  4A3C D;  4BBS D;  4DKD A;  3TGX B;  1WU3 I;  2O6I A;  3I4M D;  5D72 A;  1HIK A;  4RS1 A;  2R93 D;  2HYM B;  3NCB A;  1CN4 C;  1M48 A;  1M4C A;  2LMS A;  3UX9 A;  1NBP A;  2D9Q A;  3INK C;  1IAR A;  5C4X D;  4DKF A;  1J7V L;

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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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3H3VE

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations