4A3DD

Rna polymerase ii initial transcribing complex with a 6nt dna-rna hybrid
Total Genus 52
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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
52
sequence length
219
structure length
178
Chain Sequence
b'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 keywords DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1
publication title Structural basis of initial RNA polymerase II transcription.
pubmed doi rcsb
molecule tags Transcription
total genus 52
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; 4a3dD02
5FLMD 2JA5D 2B63D 5IYDD 4A3ED 1Y14A 4BXXD 4A3KD 4BY7D 4A93D 3H0GD 3PO3D 4BY1D 2R92D 2JA6D 3HOYD 4BBRD 4A3BD 4A3JD 4A3LD 4BBSD 1Y1VD 2JA7D 3I4ND 3AYHA 5IP7D 3HOXD 1Y1WD 3HOUD 5C44D 2R7ZD 3I4MD 5IYCD 3H3VE 4A3GD 3PO2D 5C4XD 3HOWD 4A3MD 4A3ID 5C3ED 2C35A 1WCMD 4A3DD 3FKID 5IP9D 3HOVD 4A3CD 5IYBD 2JA8D 2R93D 4A3FD 3HOZD 2VUMD
chains in the Genus database with same CATH superfamily
5FLMD 2HYMB 3WCYI 4DKEA 3SE4B 1PV6A 4BY7D 3QAZA 2O27A 1AX8A 4JA3A 5EQHA 2OQPA 1AXIA 5D22A 3HOXD 3G9VB 2B8XA 2Z3RA 4JREA 4IKXA 1RFBA 1PY2A 1HWGA 3HOVD 1ITLA 4A3FD 4GBYA 4ZYRA 2B5IA 1PW4A 1BGCA 1JLIA 1M4RA 3BPLA 4PS4A 2Y5YA 1ALUA 1A7MA 1BUYA 3NCFA 3UF5A 2Z3QA 5C44D 3OG4A 4GC0A 3SE3B 4D2CA 3OG6A 1EERA 4DKDA 3QB7A 3NCBA 2Q14A 1RCBA 4TPJA 5TS9A 3HHCA 2E9WC 4JR9A 3NCCA 1HIKA 1ETEA 1RHGA 4LDSA 1KF9A 2D48A 4YPGC 1QVNA 1FYHA 2LMSA 5EQIA 4GBZA 1YKBA 2O26A 4A3JD 2L3OA 2XUTA 1IK0A 4DOHA 1AU1A 4DKCA 4O9HA 5FHXA 4YQXA 3HOWD 2C35A 4D2DA 3HMXB 2LAGA 4EXPA 4J4LC 4A3KD 1HGUA 3PO3D 2JA6D 1BCNA 4A3LD 3OQ3A 2JA7D 1HUWA 3HHRA 4U4WA 4IKVA 3QT2C 1M4BA 1B5LA 3BPNA 3HOZD 2JA5D 2KZ1A 4NI7A 2PSMA 4APSA 4BBRD 4A3BD 4U4VA 1IJZA 1EKUA 1F45B 3EW3A 4O6KA 3I4MD 2H24A 2B8ZA 2XQBA 2CFQA 1IARA 2JA8D 1HZIA 3LB6B 2O6IA 5GXBA 5D72A 2Q7NB 5C65A 1PV7A 3L5XA 5D28B 4NN5A 2Q98A 5EQGA 4A93D 5A2NA 2B8YA 1Z92A 3MZGA 4WRLB 5FUCA 1SCFA 4ZW9A 4XNJA 2ERJD 2B8UA 4A3DD 3FKID 4A3CD 3Q1SI 4BXXD 3PIWA 4NKQC 5KNHI 1M48A 1M4CA 3HOUD 4GS7A 3PO2D 2INTA 4A3ID 1CNT1 1IL6A 4GRWA 3EJJA 2R93D 3D87A 4YBQA 4Q65A 4YUEC 4A3ED 2D9QA 3NCEA 1Y6KL 1D9CA 1P9MB 4BBSD 5IP7D 2R7ZD 4U4TA 1WU3I 4LRLA 4IU8A 3QB1A 3INKC 1GNCA 1BGDA 1V7NV 4IKWA 3O7QA 1BBNA 4BY1D 2R92D 1Y6NL 3I4ND 2ILKA 3H3VE 4TPGA 1Z7CA 1F6FA 3DI3A 1WCMD 4MHLA 2B90A 1A22A 4EXNA 4YB9D 4RS1A 1INRA 2GMFA 4ZF7A 4IKYA 3DI2A 1ITIA 5C4XD 1M47A 2CFPA 5C3ED 1CD9A 3L5WI 4IKZA 1BGEA 3G6DA 4YDYI 4TPHA 3LB6A 1HULA 4J05A 1N1FA 5IYDD 1EVSA 1CYLA 3HOYD 1ILKA 4XNIA 3PIVA 1CSGA 3IRHA 1RW5A 5IYCD 5D59A 1ITMA 1J7VL 3D85C 3TGXB 3N06A 2V8NA 3NPZA 1EMRA 4LEPA 1LKIA 1M4AA 5L6YC 2B91A 4NI9A 1FG9A 3WDOA 4QIQA 1V7MV 3QWRB 3DLQI 3S9DA 3UX9A 4UVMA 4I77Z 5C7XA 1LK3A 1GA3A 5IYBD 4Z5RD 4OH3A 4D2BA 1EXZA 3DGCL 5D70A 1LQSL 5D58A 4NEJA 4CNIC 3AYHA 3D48P 5D6KA 1D9GA 5LQBA 3VA2A 4A3MD 4OAAA 4ZWBA 5E4EA 1Y6ML 4FA8E 4ZS7A 2IL6A 3UF2A 3BPOA 1PVHB 1Y1VD 2L3YA 4IU9A 1Y1WD 1CN4C 1VLKA 4A3GD 4X51A 4NEMA 4PYPA 4ZWCA 3N0PA 1BP3A 3DUHC 4W6VA 2B63D 1Y14A 2CYKA 3H0GD 1HIJA 5A2OA 1I1RB 3UEZE 3BESL 4NN6A 4DKFA 1ITFA 1NBPA 3B5KA 1HWHA 1IRLA 5D71A 5IP9D 1M49A 4NN7A 1PGRA 1PW6A 2VUMD 3O7PA
chains in the Genus database with same CATH topology
5FLMD 2HYMB 4J4LC 3WCYI 4YUEC 4DKEA 1LKIA 3SE4B 1M4AA 5L6YC 4A3ED 2B91A 2D9QA 4A3KD 4BY7D 3QAZA 1HGUA 2O27A 3PO3D 3NCEA 1Y6KL 4NI9A 2JA6D 1BCNA 1AX8A 1FG9A 1D9CA 1P9MB 4A3LD 4EXPA 4BBSD 3OQ3A 2OQPA 2JA7D 1AXIA 1V7MV 3QWRB 5IP7D 1HUWA 5D22A 3HOXD 2R7ZD 3HHRA 3DLQI 3G9VB 3S9DA 3UX9A 2B8XA 2Z3RA 1WU3I 4LRLA 4I77Z 5C7XA 1RFBA 1PY2A 1HWGA 1LK3A 3INKC 3QB1A 3QT2C 1M4BA 5IYBD 3HOVD 1GA3A 1ITLA 4A3FD 1GNCA 1BGDA 1B5LA 1V7NV 3BPNA 4Z5RD 3HOZD 2JA5D 1EXZA 2B5IA 2KZ1A 4NI7A 3DGCL 5D70A 1LQSL 1BGCA 1BBNA 1JLIA 1M4RA 3BPLA 4PS4A 4BY1D 1ALUA 2PSMA 2R92D 1A7MA 4BBRD 1Y6NL 4A3BD 1BUYA 3NCFA 4NEJA 3I4ND 4CNIC 1IJZA 3AYHA 3UF5A 2Z3QA 5C44D 3D48P 1EKUA 2ILKA 1F45B 3OG4A 1D9GA 3EW3A 4O6KA 3H3VE 3I4MD 5LQBA 1Z7CA 2H24A 1F6FA 2B8ZA 3DI3A 3SE3B 3VA2A 2XQBA 4A3MD 1WCMD 4MHLA 1IARA 2B90A 2JA8D 1A22A 1HZIA 4EXNA 3OG6A 5E4EA 3LB6B 2O6IA 4RS1A 1EERA 4DKDA 1Y6ML 3QB7A 4FA8E 3NCBA 5D72A 2Q7NB 4ZS7A 2IL6A 3L5XA 4NN5A 5D28B 1INRA 2Q98A 3UF2A 2Q14A 4A93D 1RCBA 2B8YA 3BPOA 1PVHB 2GMFA 1Y1VD 2L3YA 5TS9A 3HHCA 2E9WC 4ZF7A 1Y1WD 1CN4C 1VLKA 3NCCA 1Z92A 1HIKA 3MZGA 1ETEA 4WRLB 4A3GD 3DI2A 5FUCA 1ITIA 1SCFA 5C4XD 1M47A 4X51A 1RHGA 4NEMA 2ERJD 5C3ED 2B8UA 4A3DD 1KF9A 1CD9A 3FKID 3N0PA 4A3CD 3L5WI 1BP3A 2D48A 1BGEA 3G6DA 3Q1SI 4YDYI 4YPGC 1QVNA 1FYHA 2LMSA 3DUHC 3LB6A 1HULA 2B63D 1N1FA 1YKBA 5IYDD 1Y14A 4BXXD 1EVSA 2CYKA 3H0GD 1CYLA 1HIJA 3PIWA 3HOYD 2O26A 4A3JD 2L3OA 4NKQC 1I1RB 5KNHI 1IK0A 1ILKA 3UEZE 1M48A 3PIVA 1CSGA 1M4CA 4DOHA 3HOUD 1AU1A 3IRHA 4GS7A 1RW5A 4DKCA 4O9HA 3BESL 5IYCD 4NN6A 5FHXA 4DKFA 1ITFA 3PO2D 1ITMA 4YQXA 1NBPA 2INTA 4A3ID 2C35A 1CNT1 1J7VL 3HOWD 1IL6A 3D85C 3TGXB 3B5KA 3N06A 4GRWA 1HWHA 1IRLA 5D71A 5IP9D 3EJJA 1M49A 4NN7A 2R93D 1PGRA 3D87A 2LAGA 1PW6A 1EMRA 3HMXB 3NPZA 2VUMD
chains in the Genus database with same CATH homology


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