4A3BD

Rna polymerase ii initial transcribing complex with a 4nt dna-rna hybrid
Total Genus 50
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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
50
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 50
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; 4a3bD02
4BBSD 4BBRD 4BY1D 3HOVD 5C4XD 4A3ID 4A93D 1Y1VD 1WCMD 4A3BD 2JA7D 3FKID 5IYCD 4A3JD 4A3CD 3I4ND 4A3DD 5C3ED 2JA6D 4A3LD 4A3FD 4BY7D 3H3VE 5IYBD 3HOXD 2B63D 4A3GD 4A3MD 3HOZD 2R92D 2VUMD 3I4MD 3H0GD 4BXXD 3PO2D 2JA5D 3AYHA 2R7ZD 4A3ED 5IP7D 1Y14A 4A3KD 3HOYD 5C44D 3PO3D 2R93D 5IP9D 1Y1WD 2C35A 5IYDD 3HOWD 5FLMD 2JA8D 3HOUD
chains in the Genus database with same CATH superfamily
1AXIA 5A2OA 4XNIA 1F6FA 4DKCA 2LMSA 4DOHA 4IU9A 2O6IA 1P9MB 5A2NA 1V7NV 3G9VB 3PIWA 3UEZE 2V8NA 1M48A 3Q1SI 2D9QA 4ZWBA 1WU3I 3NCCA 3IRHA 3BESL 3HOZD 3WDOA 1CSGA 4O9HA 1PW4A 1NBPA 4EXPA 3VA2A 5D6KA 1ITFA 5D22A 5EQIA 2JA7D 4U4TA 3HHCA 1HZIA 3UF5A 3DUHC 2OQPA 2L3YA 4GS7A 4D2CA 1Z7CA 4U4VA 4U4WA 4D2BA 5FLMD 1BBNA 4I77Z 4DKFA 1EXZA 5D70A 4A3JD 3G6DA 4TPJA 4A3FD 4GBZA 3NCEA 4W6VA 3QT2C 1J7VL 4A3KD 1IL6A 1VLKA 2R93D 3NCFA 2B8YA 4BY1D 4QIQA 1Y1VD 4A3BD 3LB6A 1HIKA 2Y5YA 4J4LC 4A3CD 4ZF7A 1HWGA 5D71A 2Z3RA 1A22A 3D85C 1IK0A 1CNT1 4GRWA 5KNHI 4D2DA 4JREA 3DGCL 5FHXA 2JA8D 1M49A 3D48P 4IU8A 3FKID 1ALUA 1M4BA 3QB1A 1PW6A 5IYBD 1I1RB 4NKQC 1Y6NL 1RHGA 1EERA 3BPOA 1GNCA 4IKYA 4IKZA 4GC0A 3HHRA 4O6KA 3D87A 2Q98A 2B91A 3N06A 3HOUD 1INRA 1BGEA 2CFPA 5D28B 1M47A 3BPNA 1HUWA 1IRLA 2D48A 4IKXA 4WRLB 2CYKA 1KF9A 4ZWCA 3PO2D 4DKDA 3OQ3A 4FA8E 5GXBA 2JA6D 2CFQA 4Z5RD 3UX9A 2B90A 1SCFA 4A3ED 5E4EA 1IARA 4NN6A 2Q14A 5D59A 4NI7A 2C35A 1BUYA 1PGRA 3UF2A 2LAGA 1V7MV 1F45B 4A3LD 4J05A 4Q65A 4CNIC 1RCBA 1HGUA 1EKUA 1PV7A 3HMXB 3O7PA 4LRLA 4IKWA 2GMFA 4YQXA 4JA3A 3DI2A 3NPZA 4BBRD 4PYPA 1CN4C 1ITIA 3BPLA 1M4RA 1FYHA 5EQHA 4APSA 1EMRA 4TPHA 4A3MD 3EJJA 2VUMD 2ILKA 4EXNA 1ITMA 4BXXD 3SE4B 1AX8A 1M4AA 4NEJA 1ITLA 2H24A 2B8XA 4PS4A 2B8ZA 2B63D 3B5KA 4NEMA 4DKEA 3DI3A 2B8UA 2HYMB 3QAZA 4BY7D 5C7XA 2R92D 1ETEA 2JA5D 2IL6A 5TS9A 2R7ZD 4LEPA 1CD9A 1Y14A 4NN5A 1QVNA 3TGXB 1A7MA 1Y1WD 1ILKA 3HOWD 4ZW9A 3HOVD 2INTA 5C65A 1EVSA 2L3OA 3H3VE 4RS1A 5LQBA 3EW3A 1PVHB 4UVMA 1LQSL 4NI9A 2Z3QA 5D58A 4X51A 3SE3B 4NN7A 2PSMA 3QB7A 3INKC 1HWHA 5C3ED 4LDSA 1BCNA 1HULA 4OAAA 3PIVA 4YDYI 1FG9A 1RW5A 3S9DA 1D9GA 3AYHA 3MZGA 4GBYA 3HOYD 1PY2A 5L6YC 2O26A 3L5WI 5IYDD 2B5IA 4YB9D 4BBSD 1GA3A 5C4XD 4A3ID 4OH3A 1M4CA 2O27A 4YBQA 1Z92A 3HOXD 4ZS7A 1N1FA 4TPGA 3H0GD 1PV6A 1BGCA 1B5LA 4MHLA 5C44D 3DLQI 3L5XA 3QWRB 4YUEC 1JLIA 1WCMD 5IYCD 5EQGA 3OG6A 1LKIA 4JR9A 1LK3A 2XUTA 4A3GD 4YPGC 3WCYI 1IJZA 3LB6B 2XQBA 4IKVA 3PO3D 1Y6KL 4XNJA 3NCBA 1HIJA 5FUCA 4A93D 1D9CA 3N0PA 1CYLA 1Y6ML 3O7QA 5D72A 3I4ND 1BGDA 2KZ1A 1AU1A 2ERJD 1YKBA 3I4MD 1RFBA 1BP3A 2Q7NB 4ZYRA 5IP7D 5IP9D 3OG4A 4A3DD 2E9WC
chains in the Genus database with same CATH topology
3SE3B 4BY1D 1AXIA 4NN7A 1Y1VD 3UF2A 3LB6A 1HIKA 2PSMA 4A3BD 1F6FA 2LAGA 4DKCA 3QB7A 4J4LC 4A3CD 3INKC 1V7MV 1HWHA 2LMSA 1F45B 4DOHA 4ZF7A 5C3ED 4A3LD 1BCNA 1HWGA 4CNIC 2O6IA 1P9MB 1RCBA 1HULA 1HGUA 3PIVA 4YDYI 1FG9A 1EKUA 1RW5A 5D71A 1V7NV 3S9DA 2Z3RA 1A22A 3D85C 1IK0A 1CNT1 1D9GA 3AYHA 3MZGA 3G9VB 4GRWA 3HMXB 5KNHI 4LRLA 2GMFA 4YQXA 3HOYD 3PIWA 1PY2A 3DI2A 5L6YC 3UEZE 2O26A 3NPZA 3L5WI 3DGCL 2B5IA 5FHXA 5IYDD 1M48A 2JA8D 3Q1SI 4BBSD 1GA3A 4BBRD 1M49A 2D9QA 5C4XD 3D48P 4A3ID 1CN4C 1M4CA 1WU3I 1ITIA 3NCCA 3BPLA 3FKID 2O27A 1M4RA 1FYHA 1ALUA 1M4BA 3QB1A 1Z92A 1PW6A 1EMRA 3IRHA 5IYBD 1I1RB 3HOXD 4ZS7A 4NKQC 1Y6NL 1N1FA 1RHGA 3BESL 3EJJA 4A3MD 1EERA 3BPOA 3H0GD 2VUMD 2ILKA 1CSGA 4EXNA 1ITMA 3HOZD 4BXXD 3SE4B 1GNCA 1AX8A 1BGCA 1M4AA 1ITLA 1B5LA 4MHLA 2H24A 4NEJA 2B8XA 4O9HA 4PS4A 5C44D 3HHRA 1NBPA 4O6KA 3D87A 4EXPA 2B8ZA 3DLQI 3VA2A 2Q98A 3L5XA 3QWRB 2B91A 2B63D 3N06A 3HOUD 3B5KA 1INRA 1BGEA 4YUEC 5D28B 1M47A 4NEMA 1ITFA 5D22A 1JLIA 1WCMD 4DKEA 3BPNA 2JA7D 3DI3A 5IYCD 1HUWA 4A3DD 3HHCA 3OG6A 1IRLA 2B8UA 1LKIA 1HZIA 3UF5A 1LK3A 2HYMB 3QAZA 4BY7D 2D48A 3DUHC 5C7XA 2OQPA 2L3YA 4WRLB 4A3GD 2CYKA 2R92D 4GS7A 4YPGC 1ETEA 3WCYI 1Z7CA 2JA5D 2IL6A 1IJZA 3LB6B 2XQBA 5TS9A 2R7ZD 1CD9A 1KF9A 1Y14A 1QVNA 4NN5A 3TGXB 3PO3D 1A7MA 1Y6KL 1Y1WD 1ILKA 3HOWD 5FLMD 1BBNA 2E9WC 3PO2D 4DKDA 3NCBA 3HOVD 4I77Z 3OQ3A 4DKFA 1HIJA 4FA8E 5FUCA 4A93D 1EXZA 1D9CA 3N0PA 2INTA 1CYLA 1Y6ML 5D70A 5D72A 4A3JD 1EVSA 3I4ND 2JA6D 3G6DA 4A3FD 1BGDA 2KZ1A 2L3OA 3H3VE 1AU1A 2ERJD 4RS1A 4Z5RD 3UX9A 5LQBA 3NCEA 3EW3A 1YKBA 3I4MD 1PVHB 2B90A 1RFBA 1BP3A 3QT2C 2Q7NB 1LQSL 1SCFA 4NI9A 4A3ED 5IP7D 1J7VL 4A3KD 5E4EA 1IL6A 1IARA 1VLKA 2R93D 5IP9D 4NN6A 2Q14A 2Z3QA 3NCFA 2C35A 4NI7A 3OG4A 2B8YA 1BUYA 4X51A 1PGRA
chains in the Genus database with same CATH homology


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