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


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