5IYCD

Human core-pic in the initial transcribing state
Total Genus 46
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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
46
sequence length
129
structure length
129
Chain Sequence
EEDASQLIFPKEFETAETLLNSEVHMLLEHRKQQNESAEDEQELSEVFMKTLNYTARFSRFKNRETIASVRSLLLQKKLHKFELACLANLCPETAEESKALIPSLEGRFEDEELQQILDDIQTKRSFQY
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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 Transcription, transferase/dna
molecule keywords DNA-directed RNA polymerase II subunit RPB1
publication title Near-atomic resolution visualization of human transcription promoter opening.
pubmed doi rcsb
source organism Homo sapiens
total genus 46
structure length 129
sequence length 129
ec nomenclature
pdb deposition date 2016-03-24

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; 5iycD00
4A3MD 4A3BD 3HOUD 2VUMD 2B63D 1Y1WD 4BXXD 4A3DD 2C35A 5IYCD 4A3JD 2JA7D 2R92D 5C44D 3HOVD 4A3LD 5C4XD 3PO2D 4BY7D 4A93D 3HOYD 3I4MD 2R93D 2R7ZD 3PO3D 5FLMD 5IP7D 2JA8D 4BBRD 2JA6D 5IP9D 4A3CD 1Y1VD 4BY1D 3HOXD 4A3ID 5C3ED 3H0GD 4A3KD 3H3VE 3I4ND 5IYBD 4A3FD 4A3GD 4A3ED 3FKID 1WCMD 3AYHA 5IYDD 2JA5D 4BBSD 1Y14A 3HOWD 3HOZD
chains in the Genus database with same CATH superfamily
1D9CA 1Y6KL 4TPJA 2INTA 4GS7A 3NCBA 3N0PA 3DI3A 3PO3D 1NBPA 4U4TA 1GA3A 4TPHA 2B8XA 3D87A 4Q65A 4BBSD 1IK0A 1I1RB 1B5LA 2XQBA 4ZW9A 2PSMA 4IKYA 2Q7NB 3UX9A 1EMRA 4QIQA 1RCBA 2LAGA 3HOVD 4GBZA 4BY7D 2Q98A 1HIKA 1V7NV 4D2BA 4LDSA 4NN7A 3HHRA 1PW4A 4NI7A 4IKVA 4A3FD 5GXBA 4LRLA 3O7PA 4DKDA 1Y1WD 2ERJD 2C35A 4WRLB 4D2CA 1HUWA 4TPGA 1Y1VD 1QVNA 2KZ1A 3DUHC 5EQIA 2IL6A 2Z3QA 3VA2A 1Z7CA 3DGCL 4O6KA 4EXPA 1IARA 5D6KA 1CYLA 3IRHA 4A93D 3OQ3A 2JA6D 1IJZA 1LK3A 3L5WI 3H0GD 3OG6A 5IYBD 2E9WC 4A3GD 3WCYI 2B8ZA 1BCNA 3BPOA 1ITFA 1AU1A 1CNT1 4J05A 1HZIA 2B91A 1WU3I 1PV7A 4U4WA 1P9MB 1RHGA 5D70A 1ITMA 4IKWA 4XNIA 3QB7A 4UVMA 4DOHA 4J4LC 3AYHA 2HYMB 3SE3B 3WDOA 3QB1A 1HGUA 1SCFA 5IP7D 4BBRD 4NEMA 1ETEA 3BPNA 1M48A 1V7MV 4OAAA 4JREA 5A2OA 1M4BA 3PIWA 1BUYA 4JR9A 1HIJA 4ZS7A 1Z92A 3NCEA 4XNJA 2B8YA 1LKIA 3I4MD 2R7ZD 1FG9A 4ZWCA 4A3ID 4CNIC 1PY2A 3FKID 1Y14A 3HOWD 5D72A 1CD9A 3DLQI 4GC0A 5EQGA 3G9VB 3INKC 1M4RA 2Z3RA 4GRWA 4IKZA 3QT2C 2OQPA 1AXIA 1VLKA 1RW5A 5C3ED 5C7XA 1CN4C 4A3ED 4PS4A 2L3OA 5C65A 4YPGC 3HOUD 1M47A 1EKUA 5FHXA 5C44D 4IKXA 3D48P 4ZF7A 5EQHA 5TS9A 3HOXD 1Y6ML 3LB6B 2B5IA 2H24A 5D58A 4NN5A 4O9HA 4ZYRA 1GNCA 2VUMD 1KF9A 2B63D 4RS1A 4IU8A 1Y6NL 5E4EA 5KNHI 1M4CA 2Q14A 1A22A 4ZWBA 4A3CD 3HMXB 4I77Z 3TGXB 4YB9D 1HWHA 4A3BD 1J7VL 4D2DA 1YKBA 3Q1SI 3B5KA 4NI9A 3HOYD 3L5XA 4PYPA 1BBNA 3MZGA 4X51A 3H3VE 4W6VA 4IU9A 1F45B 3EJJA 2JA7D 3OG4A 2R92D 4A3LD 1ALUA 5FUCA 2L3YA 4APSA 2JA8D 2CFQA 2CYKA 1EERA 2B90A 3QWRB 1F6FA 3QAZA 5IYDD 1BGDA 2D48A 4MHLA 5IYCD 1M4AA 3BESL 5C4XD 1CSGA 1HULA 1PV6A 2R93D 1ITIA 1D9GA 5D28B 4A3KD 4JA3A 2XUTA 3NCFA 1ITLA 3EW3A 3I4ND 4DKEA 1PW6A 5A2NA 1BGEA 3S9DA 4GBYA 3O7QA 3PIVA 1A7MA 3NCCA 4U4VA 5L6YC 1BP3A 3LB6A 5IP9D 1ILKA 1HWGA 4BY1D 4EXNA 5D22A 4YUEC 5LQBA 3D85C 4YQXA 2O6IA 5D59A 1PVHB 2JA5D 1IRLA 1RFBA 3BPLA 4NKQC 2ILKA 1FYHA 4A3MD 5D71A 4BXXD 4OH3A 2O27A 3N06A 4A3DD 1EVSA 4A3JD 2GMFA 2Y5YA 3HHCA 2V8NA 5FLMD 4DKFA 1PGRA 4NEJA 1EXZA 3SE4B 2CFPA 1N1FA 1JLIA 1IL6A 4YBQA 3UF2A 2B8UA 2LMSA 4NN6A 2O26A 1AX8A 3PO2D 3UEZE 3G6DA 1BGCA 4Z5RD 4YDYI 1M49A 4LEPA 4FA8E 1INRA 2D9QA 3NPZA 1LQSL 3UF5A 1WCMD 4DKCA 3DI2A 3HOZD
chains in the Genus database with same CATH topology
2D48A 1D9CA 4YPGC 2B8ZA 3HOUD 1BCNA 1M47A 1Y6KL 3BPOA 1AU1A 1CNT1 2INTA 1ITFA 4GS7A 4MHLA 1EKUA 5IYCD 4A3GD 5FHXA 1M4AA 3BESL 5C44D 1HZIA 5C4XD 1CSGA 1HULA 2B91A 3NCBA 3D48P 3N0PA 1WU3I 3DI3A 2R93D 1D9GA 4ZF7A 3PO3D 1ITIA 1NBPA 5TS9A 5D28B 1P9MB 1RHGA 3HOXD 1GA3A 4A3KD 5D70A 1Y6ML 1ITMA 2B8XA 3D87A 3LB6B 1ITLA 2B5IA 3EW3A 2H24A 3NCFA 3QB7A 3I4ND 4DKEA 4DOHA 1PW6A 4J4LC 1BGEA 3AYHA 4BBSD 1IK0A 4NN5A 1I1RB 4O9HA 3S9DA 1GNCA 1B5LA 2XQBA 2HYMB 2VUMD 1KF9A 3PIVA 2B63D 2PSMA 1A7MA 2Q7NB 3SE3B 4RS1A 1EMRA 3UX9A 3QB1A 1RCBA 2LAGA 3NCCA 1Y6NL 5E4EA 3HOVD 4BY7D 2Q98A 1HGUA 5KNHI 1M4CA 2Q14A 5L6YC 1A22A 1SCFA 1HIKA 1V7NV 5IP7D 1BP3A 3LB6A 4NN7A 4BBRD 1ILKA 1HWGA 3HHRA 3HMXB 5IP9D 4BY1D 4EXNA 4A3CD 4NEMA 4NI7A 5D22A 4YUEC 5LQBA 1ETEA 3BPNA 3D85C 4YQXA 2O6IA 4I77Z 1M48A 3TGXB 4A3FD 1PVHB 2JA5D 1IRLA 1RFBA 3BPLA 1V7MV 1HWHA 2ILKA 1FYHA 4NKQC 4A3MD 4A3BD 1J7VL 4LRLA 1M4BA 4DKDA 1YKBA 2ERJD 1BUYA 3PIWA 5D71A 1Y1WD 4BXXD 2O27A 3Q1SI 1HIJA 3B5KA 3N06A 4NI9A 2C35A 4ZS7A 1EVSA 4A3JD 4A3DD 2GMFA 1Z92A 3HHCA 3NCEA 4WRLB 2B8YA 3HOYD 1LKIA 3I4MD 2R7ZD 3L5XA 1FG9A 1HUWA 5FLMD 4DKFA 1BBNA 1Y1VD 1PGRA 4NEJA 4A3ID 1EXZA 3SE4B 3MZGA 4X51A 3H3VE 1N1FA 1QVNA 1JLIA 2KZ1A 3DUHC 4CNIC 1PY2A 1IL6A 3UF2A 3FKID 2B8UA 2IL6A 2Z3QA 1Y14A 2LMSA 4NN6A 2O26A 3HOWD 5D72A 3VA2A 1AX8A 1Z7CA 3DGCL 1CD9A 3DLQI 4O6KA 4EXPA 1IARA 3G9VB 3INKC 1M4RA 2Z3RA 4GRWA 1F45B 3EJJA 2JA7D 3OG4A 2R92D 1CYLA 3QT2C 4A3LD 3IRHA 3PO2D 1ALUA 2OQPA 5FUCA 2L3YA 4A93D 1AXIA 1VLKA 3UEZE 3G6DA 1BGCA 4Z5RD 4YDYI 3OQ3A 1M49A 2JA8D 2JA6D 1IJZA 1LK3A 2CYKA 1RW5A 3L5WI 5C3ED 4FA8E 3H0GD 1INRA 1EERA 3OG6A 5C7XA 1CN4C 5IYBD 2B90A 2D9QA 3QWRB 2E9WC 1F6FA 3NPZA 1LQSL 3UF5A 1WCMD 3QAZA 3WCYI 4DKCA 4A3ED 5IYDD 1BGDA 4PS4A 2L3OA 3DI2A 3HOZD
chains in the Genus database with same CATH homology


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