4A3CD

Rna polymerase ii initial transcribing complex with a 5nt dna-rna hybrid
Total Genus 57
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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
57
sequence length
219
structure length
178
Chain Sequence
VSTSTFQTRRRRLKKVEEEENAATLQLGQEFQLKQINHQGEEEELIALNLSEARLVIKEALVERRRAFKRSQKKTREKELESIDVLLEQTTGGNNKDLKNTMQYLTNFSRFRDQETVGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLNNKISDDELERILKELSNLETLY
Loading diagram...

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
molecule keywords DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1
publication title Structural basis of initial RNA polymerase II transcription.
pubmed doi rcsb
total genus 57
structure length 178
sequence length 219
ec nomenclature
pdb deposition date 2011-09-30

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; 4a3cD02
3HOYD 5IYCD 4BY1D 2JA7D 3HOUD 1Y1VD 3HOVD 2JA6D 2R93D 5FLMD 4BY7D 2R92D 4A3JD 3I4MD 3H3VE 2VUMD 2JA8D 3H0GD 4BBSD 2R7ZD 4A3CD 3PO3D 5IYBD 5C3ED 1Y1WD 1WCMD 2C35A 3PO2D 5C4XD 2B63D 2JA5D 3HOZD 3I4ND 4BXXD 3AYHA 4A3ED 4A3MD 5C44D 1Y14A 3HOXD 4A93D 4A3LD 5IP7D 4A3BD 4A3GD 5IP9D 4A3KD 4BBRD 4A3DD 3FKID 4A3FD 4A3ID 5IYDD 3HOWD
chains in the Genus database with same CATH superfamily
3NCBA 1IL6A 4NEJA 3BPOA 1M4AA 4D2BA 4BY1D 2Q98A 4D2CA 3O7QA 4ZYRA 3L5XA 3H3VE 1PW4A 4JA3A 5D22A 3PIVA 4YB9D 4D2DA 2JA5D 4JREA 3PIWA 2CFPA 4A93D 1RW5A 1AXIA 3OQ3A 5D28B 3HOWD 1HWHA 5E4EA 3HHCA 4A3CD 3WCYI 1M4BA 3D85C 5FUCA 1NBPA 1Z7CA 3OG6A 4A3ED 4NEMA 4A3LD 3UX9A 4A3FD 5L6YC 5D59A 1HIJA 3PO2D 1PY2A 5KNHI 3TGXB 4FA8E 4OAAA 3SE4B 3WDOA 4NI9A 4A3MD 2CYKA 3D87A 4TPJA 5IP7D 4A3BD 2L3OA 4XNIA 3LB6A 2ERJD 1Y1VD 5EQIA 4IU9A 3IRHA 3H0GD 3HHRA 5C3ED 1ITFA 4U4WA 3O7PA 3N06A 1HZIA 3FKID 1FG9A 1BCNA 3HOYD 5D6KA 4QIQA 5EQGA 3UEZE 4DOHA 2B5IA 1A22A 1RFBA 4YPGC 4EXPA 1V7NV 3LB6B 4LDSA 3DUHC 1PW6A 2OQPA 3UF5A 1CSGA 2E9WC 2GMFA 4ZS7A 4YUEC 1LQSL 4A3DD 2Q14A 5D70A 1V7MV 1I1RB 1JLIA 2XUTA 1CN4C 1HULA 4GBYA 1GNCA 4GBZA 1RCBA 3NCFA 1BGCA 1WCMD 1M47A 3DLQI 5TS9A 4IKZA 4WRLB 1Y6NL 1ALUA 3DI3A 1YKBA 4A3KD 4OH3A 1Y6KL 4A3ID 4NN6A 1LK3A 1RHGA 1VLKA 3HOUD 4ZF7A 1D9CA 4BY7D 1SCFA 4DKFA 4PYPA 1AU1A 3Q1SI 1EMRA 5C4XD 4ZWCA 1D9GA 4RS1A 3SE3B 2INTA 1BP3A 4DKDA 4IKYA 4J05A 4Q65A 4O6KA 2Q7NB 3MZGA 2Z3QA 5D71A 5A2NA 1EKUA 5IYBD 3D48P 4NI7A 1IJZA 2ILKA 2O6IA 3QWRB 3NCEA 4I77Z 1AX8A 5GXBA 1WU3I 1FYHA 5D58A 2R7ZD 1HWGA 2B91A 5IP9D 1BUYA 3N0PA 1ITMA 1F45B 1PV6A 4IKVA 1CYLA 1BGDA 3DGCL 2JA7D 1Z92A 1ITIA 5FLMD 3I4MD 4JR9A 4U4TA 3S9DA 3EW3A 3INKC 1M48A 1PV7A 1ETEA 1A7MA 4A3GD 4PS4A 1J7VL 2H24A 1EVSA 1KF9A 2HYMB 4YQXA 2CFQA 4NN7A 1PVHB 1PGRA 2R92D 3UF2A 1IRLA 2B90A 4IKXA 2IL6A 2B8XA 3VA2A 4LEPA 3AYHA 4TPGA 1HGUA 3QAZA 2PSMA 4ZW9A 1IK0A 1M49A 1INRA 1Y6ML 4DKEA 3BPLA 4A3JD 3NCCA 3QB7A 3DI2A 5C7XA 4GRWA 4W6VA 3BESL 4X51A 3I4ND 1N1FA 3G6DA 1EXZA 4EXNA 3HOXD 1M4RA 2B8ZA 2O27A 1ITLA 4BBRD 5IYDD 4DKCA 2JA6D 4IU8A 4UVMA 2LMSA 2JA8D 3PO3D 1Y1WD 3OG4A 1M4CA 1LKIA 4XNJA 4O9HA 2LAGA 5C44D 1EERA 5IYCD 2L3YA 3G9VB 1B5LA 2B8YA 2XQBA 1F6FA 1ILKA 3L5WI 3EJJA 4IKWA 1BGEA 2D9QA 4APSA 4TPHA 4BXXD 3NPZA 2KZ1A 1Y14A 5A2OA 2V8NA 4J4LC 4ZWBA 2Z3RA 2D48A 3B5KA 4YDYI 3HOVD 5C65A 2Y5YA 5FHXA 4BBSD 2B8UA 2C35A 3BPNA 2O26A 4MHLA 3HOZD 1IARA 4Z5RD 1HIKA 3HMXB 2R93D 3QT2C 4U4VA 1CNT1 2VUMD 1GA3A 5D72A 4GC0A 4NN5A 4YBQA 5EQHA 4CNIC 2B63D 4GS7A 1P9MB 1CD9A 1QVNA 4LRLA 1BBNA 1HUWA 3QB1A 4NKQC 5LQBA
chains in the Genus database with same CATH topology
3NCBA 1IL6A 4NEJA 3HOYD 3BPOA 1M4AA 4BY1D 4DKCA 2Q98A 1WU3I 2JA6D 1FYHA 3UEZE 4DOHA 2B5IA 2LMSA 3L5XA 3H3VE 1A22A 1RFBA 4YPGC 2JA8D 4EXPA 2R7ZD 3PO3D 1V7NV 1HWGA 5D22A 1Y1WD 3OG4A 1M4CA 3PIVA 1LKIA 3LB6B 3DUHC 4O9HA 1PW6A 2OQPA 2JA5D 3UF5A 3PIWA 2LAGA 5C44D 1CSGA 2E9WC 2GMFA 2B91A 1EERA 4ZS7A 4A93D 4YUEC 1LQSL 1RW5A 5IP9D 4A3DD 1AXIA 2Q14A 1BUYA 3N0PA 1ITMA 1F45B 5D70A 3OQ3A 1CYLA 5D28B 3HOWD 1HWHA 1V7MV 1BGDA 1I1RB 5IYCD 2L3YA 3DGCL 2JA7D 1JLIA 5E4EA 3HHCA 1Z92A 1ITIA 1CN4C 5FLMD 3G9VB 1B5LA 2B8YA 1HULA 3I4MD 2XQBA 1GNCA 1F6FA 1ILKA 3L5WI 1RCBA 4A3CD 3EJJA 3NCFA 1BGCA 1BGEA 1WCMD 1M47A 3WCYI 3DLQI 3S9DA 1M4BA 3D85C 2D9QA 5FUCA 1NBPA 1Z7CA 5TS9A 3EW3A 3INKC 4BXXD 3NPZA 3OG6A 1Y6NL 4NEMA 4WRLB 2KZ1A 1Y14A 4A3ED 4A3LD 1ALUA 1M48A 3DI3A 1A7MA 1ETEA 4A3GD 4PS4A 4J4LC 3UX9A 1YKBA 2Z3RA 4A3KD 2D48A 1J7VL 1Y6KL 2H24A 3B5KA 5L6YC 4A3FD 4A3ID 1EVSA 4NN6A 1KF9A 1HIJA 4YDYI 3PO2D 1PY2A 2HYMB 1LK3A 1RHGA 1VLKA 5KNHI 4ZF7A 3HOUD 1D9CA 4YQXA 4NN7A 3TGXB 3HOVD 4BY7D 1PVHB 1PGRA 2R92D 3UF2A 1IRLA 4FA8E 1SCFA 2B90A 5FHXA 4BBSD 3SE4B 4DKFA 1AU1A 2IL6A 2B8UA 2C35A 2B8XA 3Q1SI 3VA2A 3BPNA 1EMRA 2O26A 5C4XD 4MHLA 3HOZD 1D9GA 4NI9A 3AYHA 4A3MD 4RS1A 2CYKA 3D87A 3SE3B 5IP7D 4A3BD 1IARA 1HGUA 2INTA 3QAZA 2L3OA 1BP3A 4Z5RD 1HIKA 4DKDA 2PSMA 3HMXB 3LB6A 1IK0A 4O6KA 2Q7NB 1M49A 2ERJD 3MZGA 2Z3QA 1INRA 1Y1VD 5D71A 2R93D 1Y6ML 3QT2C 4DKEA 3BPLA 4A3JD 1CNT1 3IRHA 1EKUA 2VUMD 5D72A 1GA3A 3H0GD 3HHRA 5IYBD 3D48P 4NN5A 3NCCA 3QB7A 3DI2A 5C3ED 4NI7A 5C7XA 1IJZA 4GRWA 4CNIC 1ITFA 2ILKA 3BESL 4X51A 2B63D 3I4ND 1N1FA 1P9MB 2O6IA 3QWRB 4GS7A 1CD9A 1EXZA 1QVNA 3G6DA 1M4RA 2B8ZA 2O27A 4EXNA 3HOXD 4LRLA 1ITLA 3NCEA 1BBNA 3N06A 4I77Z 1AX8A 1HZIA 4BBRD 3FKID 1HUWA 1FG9A 3QB1A 4NKQC 1BCNA 5LQBA 5IYDD
chains in the Genus database with same CATH homology


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