4A3KD

Rna polymerase ii initial transcribing complex with a 7nt dna-rna hybrid
Total Genus 54
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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
54
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 54
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; 4a3kD02
2C35A 4A3ED 3AYHA 5IP7D 4A93D 1Y14A 2JA7D 3HOZD 4A3KD 2VUMD 3HOUD 2R7ZD 5IP9D 4A3LD 2R93D 3HOVD 2R92D 2B63D 5IYBD 3I4MD 4BBSD 4A3DD 3HOWD 4A3CD 3PO2D 4A3GD 2JA5D 4A3ID 3HOYD 5IYDD 1Y1WD 2JA6D 3HOXD 3I4ND 2JA8D 1Y1VD 3FKID 4A3FD 4A3MD 4BY7D 5C3ED 4BBRD 4BY1D 5C44D 4BXXD 5IYCD 3PO3D 4A3BD 1WCMD 5C4XD 3H0GD 5FLMD 3H3VE 4A3JD
chains in the Genus database with same CATH superfamily
4XNJA 2E9WC 4MHLA 1RHGA 5D28B 3HOZD 1Y6KL 2B91A 3EW3A 1M4CA 4BBSD 4GS7A 4IKYA 4J4LC 1AXIA 1IARA 1HULA 5KNHI 3DI3A 3PO3D 1CYLA 2O26A 5C4XD 4YPGC 4A3ED 1RFBA 2Q7NB 2ERJD 3PIVA 1ILKA 2B8XA 4JA3A 3I4MD 4A3DD 4CNIC 2B8ZA 3IRHA 4YB9D 1Y1VD 3QB7A 4Z5RD 3DGCL 3S9DA 1LQSL 3N0PA 2VUMD 5D58A 4DKCA 1M49A 4APSA 3B5KA 2B8YA 4A3GD 1EXZA 1D9CA 1N1FA 2JA6D 4NI7A 1BCNA 4RS1A 4TPGA 4BY7D 4IKXA 1HIJA 5EQIA 4YBQA 1Z92A 1FG9A 4A3JD 2V8NA 1BGCA 4J05A 4FA8E 3HOWD 5D72A 4WRLB 2B5IA 3QT2C 2D48A 1HUWA 3O7PA 4ZS7A 4IKWA 1D9GA 1WCMD 1INRA 1YKBA 5FLMD 1AX8A 5A2NA 3AYHA 1Y14A 4TPHA 2B8UA 4U4VA 3HHCA 4D2BA 1PY2A 1JLIA 1EERA 1PV6A 4NN6A 3NCFA 3BPOA 1HZIA 4ZW9A 2H24A 3OG4A 4DKDA 1LK3A 3INKC 2L3OA 1BP3A 1BGEA 4GRWA 3HHRA 5IP9D 1QVNA 4NEMA 2IL6A 2B63D 1V7NV 1M4BA 1RW5A 3O7QA 3FKID 1CN4C 1PW6A 4A3MD 1BGDA 5LQBA 4U4WA 1EKUA 4NEJA 2CFQA 4LRLA 3G6DA 4GC0A 1PVHB 1PGRA 1F45B 4IKVA 3EJJA 4A3FD 4W6VA 4Q65A 2O6IA 3UX9A 2CFPA 4IU8A 3NCEA 4GBYA 3H3VE 4OH3A 3WDOA 4A3KD 1BUYA 3VA2A 1IK0A 5C7XA 1A7MA 1PV7A 3DUHC 4YQXA 5C3ED 4BBRD 3BPNA 3D87A 1ITLA 1EVSA 3LB6A 2R7ZD 5A2OA 2L3YA 1ITIA 2JA5D 4A3ID 1PW4A 5D70A 5IYDD 3UF2A 3OQ3A 1LKIA 3WCYI 4BXXD 4A3BD 1P9MB 3H0GD 4O9HA 5D22A 3HMXB 1A22A 2R93D 1F6FA 1M4AA 4JR9A 5IYBD 4PS4A 1HWHA 3QAZA 1V7MV 1FYHA 2B90A 3L5WI 5C44D 4LEPA 5L6YC 5D6KA 3LB6B 2JA7D 4UVMA 1M48A 4NN5A 2GMFA 1AU1A 2Z3RA 1M47A 3I4ND 5TS9A 5EQGA 3SE3B 3DI2A 3NCCA 2O27A 4D2DA 2CYKA 3NCBA 4A93D 1J7VL 1M4RA 1B5LA 1CSGA 1WU3I 3G9VB 1I1RB 2INTA 3SE4B 1HIKA 2KZ1A 4IKZA 4I77Z 3PIWA 4U4TA 2PSMA 3QB1A 3MZGA 5D71A 4NKQC 3Q1SI 3BPLA 2HYMB 2Z3QA 1Y6NL 2R92D 4IU9A 1Y6ML 4A3CD 5EQHA 1GNCA 2XUTA 4YUEC 3N06A 3QWRB 3NPZA 4TPJA 2JA8D 1GA3A 3UF5A 1ITFA 1VLKA 2Y5YA 1ETEA 4D2CA 5IP7D 2Q98A 3D48P 5GXBA 4A3LD 3HOVD 4ZF7A 3BESL 4OAAA 3D85C 3PO2D 1SCFA 3HOYD 5FUCA 3HOXD 1IL6A 3UEZE 4ZWCA 4DKEA 4BY1D 5IYCD 1NBPA 1KF9A 1IJZA 4DKFA 3HOUD 3L5XA 5D59A 2LAGA 1Z7CA 1ITMA 4JREA 4GBZA 1CNT1 4LDSA 1BBNA 4EXNA 4XNIA 5FHXA 1Y1WD 5E4EA 1RCBA 3OG6A 1EMRA 1ALUA 4ZWBA 4ZYRA 4NI9A 4O6KA 2LMSA 3TGXB 1IRLA 4X51A 4DOHA 2OQPA 2C35A 4YDYI 3DLQI 4EXPA 2XQBA 4PYPA 4NN7A 4QIQA 1HGUA 2D9QA 2ILKA 1HWGA 5C65A 1CD9A 2Q14A
chains in the Genus database with same CATH topology
3QB1A 3MZGA 5D71A 3AYHA 4NKQC 3Q1SI 3LB6A 2E9WC 3BPLA 1Y14A 4MHLA 1RHGA 2B8UA 5D28B 3HOZD 1Y6KL 3HHCA 2R7ZD 2HYMB 2Z3QA 2L3YA 1Y6NL 2R92D 2B91A 3EW3A 1PY2A 1Y6ML 1M4CA 4BBSD 4GS7A 4A3CD 1ITIA 4J4LC 1GNCA 4YUEC 3N06A 3QWRB 4A3ID 1JLIA 2JA5D 1EERA 1AXIA 5D70A 5IYDD 3UF2A 4NN6A 3NCFA 3NPZA 3OQ3A 2JA8D 1IARA 1GA3A 1HULA 3BPOA 1HZIA 3UF5A 5KNHI 3DI3A 1LKIA 3WCYI 1ITFA 4BXXD 1VLKA 3PO3D 1CYLA 2O26A 4A3BD 5C4XD 4YPGC 1P9MB 3H0GD 2H24A 4O9HA 4A3ED 1ETEA 3HMXB 1RFBA 5D22A 1A22A 3OG4A 5IP7D 2Q7NB 4DKDA 1LK3A 2ERJD 2Q98A 3INKC 2L3OA 1BP3A 1BGEA 3PIVA 4GRWA 1ILKA 3D48P 1F6FA 3HHRA 5IP9D 4A3LD 1QVNA 2B8XA 1M4AA 4NEMA 3HOVD 2IL6A 4ZF7A 5IYBD 3I4MD 2B63D 3BESL 1V7NV 3D85C 4A3DD 4CNIC 3PO2D 1SCFA 2B8ZA 4PS4A 3IRHA 1HWHA 3HOYD 1M4BA 1RW5A 3QAZA 5FUCA 3HOXD 1Y1VD 3FKID 1IL6A 3UEZE 3QB7A 4Z5RD 1CN4C 1PW6A 4A3MD 3DGCL 1V7MV 1FYHA 4DKEA 2B90A 1BGDA 3L5WI 5IYCD 5C44D 4BY1D 3S9DA 5LQBA 1LQSL 5FLMD 1EKUA 1NBPA 3N0PA 4NEJA 4LRLA 3G6DA 5L6YC 1KF9A 1IJZA 3LB6B 1PVHB 4DKFA 2JA7D 2VUMD 3HOUD 3L5XA 2LAGA 4DKCA 1M49A 1M48A 1Z7CA 1ITMA 4NN5A 1CNT1 3B5KA 2B8YA 4A3GD 1BBNA 2GMFA 1PGRA 1AU1A 2Z3RA 4EXNA 1EXZA 1M47A 5FHXA 1D9CA 1F45B 1N1FA 1Y1WD 2JA6D 3EJJA 5E4EA 1RCBA 4NI7A 3I4ND 3OG6A 4A3FD 1BCNA 5TS9A 4RS1A 1EMRA 1ALUA 4NI9A 4BY7D 4O6KA 2LMSA 1HIJA 3TGXB 1IRLA 4X51A 3SE3B 4DOHA 1Z92A 2R93D 2O6IA 2OQPA 1FG9A 3DI2A 2O27A 3NCCA 3UX9A 4A3JD 3NCEA 3H3VE 2C35A 2CYKA 4YDYI 3NCBA 4A93D 1BGCA 1J7VL 1M4RA 1B5LA 3DLQI 4EXPA 4A3KD 1CSGA 1BUYA 1WU3I 3VA2A 1IK0A 4FA8E 2XQBA 3HOWD 5C7XA 1A7MA 3G9VB 1I1RB 2INTA 3DUHC 4NN7A 4YQXA 5D72A 4WRLB 2B5IA 3QT2C 1HGUA 2D48A 3SE4B 1HUWA 1HIKA 2KZ1A 2D9QA 4ZS7A 2ILKA 4I77Z 5C3ED 4BBRD 3BPNA 3D87A 3PIWA 1ITLA 1HWGA 1D9GA 1EVSA 1WCMD 2PSMA 1INRA 1YKBA 1CD9A 1AX8A 2Q14A
chains in the Genus database with same CATH homology


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