5C3ED

Crystal structure of a transcribing rna polymerase ii complex reveals a complete transcription bubble
Total Genus 43
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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
43
sequence length
218
structure length
178
Chain Sequence
STSTFQTRRRRLKKVEEEENAATLQLGQEFQLKQINHQGEEEELIALNLSEARLVIKEALVERRRAFKRSQKKETREKELESIDVLLEQTTGGNNKDLKNTMQYLTNFSRFRDQETVGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLNNKISDDELERILKELSNLETLY
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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 tags Transferase/dna/rna
molecule keywords DNA-directed RNA polymerase II subunit RPB1
publication title Crystal Structure of a Transcribing RNA Polymerase II Complex Reveals a Complete Transcription Bubble.
pubmed doi rcsb
source organism Saccharomyces cerevisiae (strain atcc 204508 / s288c)
total genus 43
structure length 178
sequence length 218
ec nomenclature
pdb deposition date 2015-06-17

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
D PF03874 RNA_pol_Rpb4 RNA polymerase Rpb4
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
1.20.1250.40 Mainly Alpha Up-down Bundle Growth Hormone; Chain: A; Growth Hormone; Chain: A; 5c3eD02
2JA8D 4A3DD 2C35A 3H0GD 2R7ZD 4A3CD 4BBSD 4BXXD 5IYDD 2JA7D 4A3FD 1Y1WD 3PO2D 2VUMD 4BY7D 4A3GD 3FKID 3HOZD 4A3ED 3AYHA 3I4MD 5FLMD 5C3ED 1Y1VD 3PO3D 5IP7D 5C44D 4A3KD 5IYBD 3HOYD 3HOUD 5C4XD 5IP9D 1WCMD 1Y14A 4A3JD 4A3ID 2JA6D 3H3VE 3HOWD 2JA5D 4A3MD 2R92D 3I4ND 3HOVD 2B63D 4A3LD 5IYCD 4A3BD 4BBRD 4A93D 3HOXD 2R93D 4BY1D
chains in the Genus database with same CATH superfamily
2D48A 3HHRA 2Q7NB 5FHXA 3L5XA 1BGCA 4NN6A 4ZWCA 1ITFA 4JA3A 4FA8E 3O7QA 2V8NA 4ZYRA 1SCFA 4PYPA 4D2CA 3G9VB 3INKC 4NI9A 2CYKA 3NCFA 2IL6A 3HOZD 4IKVA 2B8UA 4APSA 3D85C 4YBQA 5C44D 4JR9A 1N1FA 4JREA 4Q65A 2JA8D 4WRLB 1CYLA 2LAGA 4GRWA 3FKID 3UF2A 4EXNA 1BBNA 2OQPA 2GMFA 4D2BA 3DI3A 3QB1A 5D70A 4TPHA 1ITMA 1PY2A 1LKIA 3SE4B 1BGDA 5GXBA 3HOXD 1RW5A 2R93D 5D72A 1M4CA 1IJZA 2H24A 1GNCA 1FG9A 3OQ3A 4IKZA 1HIKA 2VUMD 1RCBA 4A3ED 1PV7A 3I4MD 1RHGA 5A2OA 3LB6B 2B90A 1NBPA 4RS1A 1QVNA 1I1RB 4TPJA 1F45B 3HOUD 4OAAA 3H3VE 4NEJA 1Y6ML 1HGUA 1IK0A 4BY7D 3NCEA 1M4BA 2Q14A 4O6KA 4YQXA 5FUCA 4MHLA 1BCNA 5D71A 3BPOA 1ITLA 1PW4A 4BXXD 5IYDD 2Z3QA 5KNHI 4DOHA 2XUTA 1BGEA 2O27A 3TGXB 1GA3A 3N06A 1EMRA 3BESL 4NN7A 2R92D 4XNIA 3HMXB 4GS7A 3D87A 3DUHC 1B5LA 1PVHB 4BBSD 2JA7D 1INRA 4IKXA 5D28B 1Z7CA 1M4AA 1JLIA 1VLKA 3NCCA 1A7MA 3HOYD 5C4XD 1BUYA 4A3JD 5E4EA 2L3OA 3I4ND 1A22A 3BPNA 4BY1D 3Q1SI 4ZWBA 2XQBA 5D6KA 4EXPA 1M49A 1EKUA 4DKEA 4IKYA 4X51A 3PO3D 4YPGC 3UF5A 2PSMA 4CNIC 1F6FA 1WU3I 4ZS7A 5C7XA 2Z3RA 4A3CD 3D48P 2ERJD 3PO2D 4U4WA 5D58A 5FLMD 1D9CA 5D22A 4Z5RD 3EW3A 1CSGA 4DKFA 3QWRB 4A3BD 1IRLA 2C35A 4I77Z 3IRHA 3G6DA 2D9QA 2KZ1A 1LQSL 4LEPA 1WCMD 1AU1A 4A3ID 4DKDA 4D2DA 4TPGA 1CD9A 4A3DD 1PW6A 1KF9A 3VA2A 1M47A 4A3FD 3DI2A 4NI7A 4PS4A 1AX8A 1Y1VD 1V7NV 1HUWA 1M48A 3WDOA 2Y5YA 1IL6A 4J05A 1HIJA 4GBYA 5EQIA 4J4LC 1HWHA 3HHCA 1J7VL 3H0GD 1ETEA 1Y6KL 4LDSA 4IU8A 3L5WI 4GBZA 5TS9A 4GC0A 3DGCL 2B8YA 1HZIA 5D59A 4A3KD 4QIQA 3BPLA 1LK3A 4IU9A 1Y14A 2L3YA 4A3MD 3UX9A 4A93D 1EVSA 1YKBA 2O26A 3UEZE 4NN5A 1BP3A 2E9WC 3QAZA 5C3ED 4NEMA 2HYMB 1HWGA 5IYBD 2O6IA 3OG4A 5LQBA 5IP9D 3HOWD 2JA5D 2LMSA 4IKWA 5EQHA 3S9DA 5IYCD 3OG6A 4BBRD 5C65A 1D9GA 3LB6A 4DKCA 1P9MB 4W6VA 3EJJA 3DLQI 1CNT1 1Y6NL 2ILKA 4YDYI 3NCBA 4LRLA 1RFBA 3QT2C 3NPZA 4A3LD 4ZF7A 1PGRA 5A2NA 4YUEC 4OH3A 4O9HA 1Y1WD 5EQGA 3MZGA 1ITIA 2INTA 3PIVA 5IP7D 5L6YC 3O7PA 2B8ZA 3N0PA 2B5IA 3B5KA 2JA6D 2B8XA 4YB9D 1HULA 1FYHA 1M4RA 1EERA 3SE3B 3PIWA 3WCYI 1AXIA 2CFPA 4UVMA 1CN4C 2R7ZD 1Z92A 4U4VA 4A3GD 1PV6A 4XNJA 2B91A 2Q98A 3AYHA 4ZW9A 1ALUA 4U4TA 1ILKA 2CFQA 1EXZA 4NKQC 3QB7A 1V7MV 3HOVD 2B63D 1IARA
chains in the Genus database with same CATH topology
1YKBA 2O26A 2Z3RA 3UEZE 4A3CD 3D48P 4NN5A 2ERJD 1BP3A 2D48A 2E9WC 1IK0A 3PO2D 4BY7D 3HHRA 2Q7NB 3QAZA 3NCEA 5FHXA 3L5XA 1BGCA 4NN6A 5FLMD 1D9CA 5C3ED 1ITFA 1M4BA 2HYMB 4NEMA 2Q14A 5D22A 4O6KA 1HWGA 4Z5RD 5IYBD 4A93D 4YQXA 2O6IA 3OG4A 4MHLA 5FUCA 4FA8E 5LQBA 1BCNA 5D71A 5IP9D 3EW3A 3HOWD 1CSGA 2JA5D 1SCFA 3BPOA 1ITLA 2LMSA 4DKFA 3QWRB 3G9VB 3INKC 3S9DA 1IRLA 5IYCD 3OG6A 4BBRD 4A3BD 1D9GA 2C35A 3LB6A 4I77Z 3IRHA 4DKCA 4NI9A 2CYKA 3G6DA 1P9MB 3NCFA 4BXXD 2IL6A 5IYDD 2Z3QA 5KNHI 4DOHA 3HOZD 2B8UA 2D9QA 2KZ1A 3D85C 3EJJA 1BGEA 1LQSL 2O27A 3TGXB 3DLQI 1CNT1 1GA3A 1Y6NL 3N06A 5C44D 2ILKA 1EMRA 3BESL 4YDYI 1WCMD 1AU1A 3NCBA 4LRLA 1RFBA 4NN7A 4A3ID 4DKDA 3QT2C 3NPZA 2R92D 1N1FA 4A3LD 4ZF7A 1PGRA 3HMXB 4GS7A 3D87A 3DUHC 1CD9A 1B5LA 2JA8D 4WRLB 1PW6A 4YUEC 2LAGA 4A3DD 1PVHB 1CYLA 1KF9A 4GRWA 3VA2A 4BBSD 1M47A 2JA7D 1INRA 4O9HA 4A3FD 1Y1WD 3DI2A 3MZGA 3FKID 3UF2A 4EXNA 1BBNA 5D28B 4NI7A 2INTA 4PS4A 2OQPA 1ITIA 1Z7CA 1AX8A 3PIVA 1Y1VD 2GMFA 1V7NV 5IP7D 1HUWA 1M4AA 1JLIA 1M48A 1VLKA 3NCCA 5L6YC 3DI3A 2B8ZA 3QB1A 1IL6A 3N0PA 1HIJA 1A7MA 3HOYD 5D70A 2B5IA 3B5KA 5C4XD 1BUYA 1ITMA 4A3JD 5E4EA 1PY2A 2B8XA 2JA6D 2L3OA 1LKIA 1HULA 4J4LC 1HWHA 3I4ND 3SE4B 1A22A 1FYHA 1M4RA 1BGDA 1EERA 3BPNA 3HHCA 1J7VL 3SE3B 3H0GD 1RW5A 3HOXD 2R93D 3PIWA 5D72A 1AXIA 1ETEA 1Y6KL 3Q1SI 3WCYI 4BY1D 1CN4C 1M4CA 2R7ZD 1IJZA 1Z92A 2H24A 1GNCA 1FG9A 3OQ3A 2XQBA 3L5WI 4EXPA 1HIKA 2VUMD 1RCBA 4A3GD 1M49A 1EKUA 4DKEA 4A3ED 5TS9A 2B91A 2Q98A 3AYHA 3I4MD 3DGCL 2B8YA 1RHGA 4X51A 1HZIA 3LB6B 4YPGC 3UF5A 1ALUA 2B90A 3PO3D 1ILKA 1NBPA 4RS1A 4A3KD 1QVNA 3BPLA 1I1RB 1F45B 1EXZA 1LK3A 4NKQC 3HOUD 3QB7A 2PSMA 1Y14A 4CNIC 3H3VE 2L3YA 1V7MV 4NEJA 1F6FA 4A3MD 3HOVD 2B63D 1IARA 1WU3I 1Y6ML 3UX9A 4ZS7A 1HGUA 5C7XA 1EVSA
chains in the Genus database with same CATH homology


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