4A3ID

Rna polymerase ii binary complex with dna
Total Genus 47
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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
47
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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publication title Structural basis of initial RNA polymerase II transcription.
pubmed doi rcsb
molecule keywords DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1
molecule tags Transcription
total genus 47
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; 4a3iD02
5IP9D 4A3ED 2R93D 4A3KD 2JA5D 4A3LD 1Y1WD 5IYBD 2JA8D 4A3ID 3HOVD 5C4XD 2C35A 3HOXD 4A3JD 4A3BD 3H0GD 4BY1D 4A3MD 5C44D 3H3VE 1WCMD 3I4ND 4BY7D 4A93D 2B63D 5C3ED 5IYDD 2R92D 2JA7D 3HOWD 2JA6D 5FLMD 4BBRD 3I4MD 5IYCD 3PO3D 1Y1VD 2VUMD 3HOUD 3HOYD 3PO2D 2R7ZD 1Y14A 3FKID 4A3DD 3AYHA 4A3GD 4A3FD 3HOZD 4BBSD 5IP7D 4A3CD 4BXXD
chains in the Genus database with same CATH superfamily
5D28B 2JA5D 4NKQC 1EKUA 3OQ3A 4IKXA 1BBNA 2D9QA 4A3MD 1CN4C 3PIWA 1ITIA 4U4WA 2VUMD 2Z3RA 2HYMB 4IKYA 3PO2D 1J7VL 1P9MB 1BGEA 4RS1A 4GBYA 1I1RB 4ZYRA 4A3FD 3LB6A 5IP9D 1Y1WD 5TS9A 2B5IA 2Q7NB 2B63D 1IJZA 4ZF7A 2L3OA 2Y5YA 1D9GA 4O6KA 4YPGC 3HHRA 3NCBA 4PYPA 4JR9A 1PGRA 3QWRB 1RHGA 4A3JD 5D72A 5EQIA 4GBZA 1IRLA 3HHCA 2B90A 1EXZA 3HOYD 2R7ZD 5A2OA 1VLKA 1CNT1 1YKBA 4A3ED 3BPLA 1CSGA 4NEMA 4XNJA 1BP3A 1BCNA 1V7NV 3LB6B 3PO3D 5LQBA 3Q1SI 1Y14A 3NCCA 3QB1A 1HIKA 5IP7D 5A2NA 5D22A 4D2BA 3VA2A 2B8ZA 4YDYI 3HOVD 4GS7A 2CYKA 4Z5RD 3SE3B 4A3BD 3EJJA 1RW5A 1WCMD 3QT2C 1HWHA 3NPZA 1Y6KL 4DKDA 4EXNA 2CFQA 5IYCD 1BUYA 1FG9A 1IARA 3N0PA 3FKID 3OG4A 3O7PA 4DKFA 3G6DA 4U4TA 4EXPA 1HWGA 1BGCA 4A3KD 5D70A 4A3LD 3UF5A 1Y6ML 3HOXD 1IK0A 2KZ1A 1ITMA 1WU3I 1ALUA 3SE4B 3WDOA 5FLMD 4YQXA 2L3YA 5C7XA 3BPOA 4TPGA 5GXBA 4APSA 4X51A 4J05A 4QIQA 2D48A 4IKVA 3B5KA 3QB7A 5C4XD 1D9CA 1M47A 1EERA 3I4ND 1ITLA 3DLQI 4DKCA 4FA8E 3DI3A 4IU9A 3HOUD 1HGUA 3NCFA 4IKWA 3HOZD 2Q98A 3L5WI 5KNHI 3H0GD 1FYHA 3D85C 4J4LC 1PVHB 1RFBA 4ZWBA 4OH3A 3HOWD 1PY2A 4BBRD 3D87A 4I77Z 3G9VB 1Z92A 5EQHA 4NN5A 1M49A 1SCFA 4GC0A 3QAZA 2INTA 3UEZE 4ZW9A 4BXXD 1JLIA 1F45B 3MZGA 2PSMA 3TGXB 4YBQA 2GMFA 1EMRA 4DOHA 1GA3A 3D48P 1HZIA 2R92D 1M4AA 4PS4A 1B5LA 4ZS7A 2XUTA 2CFPA 1PW6A 2OQPA 1Z7CA 1INRA 3DGCL 1HULA 4D2DA 3HMXB 1ETEA 5C44D 2V8NA 5FUCA 1KF9A 4D2CA 2ERJD 1GNCA 1HIJA 1N1FA 3AYHA 4CNIC 4NN7A 4U4VA 2H24A 1LKIA 5D58A 2O26A 5IYBD 3EW3A 2JA8D 4TPJA 1CD9A 4GRWA 4LEPA 4BY7D 3BPNA 1Y6NL 3OG6A 1HUWA 1IL6A 4YUEC 2B8YA 3IRHA 4O9HA 4MHLA 2B8UA 1V7MV 2C35A 3BESL 4W6VA 4NI9A 4JA3A 3L5XA 5IYDD 3N06A 4TPHA 2Z3QA 1LK3A 2IL6A 2O6IA 4XNIA 1AU1A 2E9WC 2B91A 4LDSA 1F6FA 4ZWCA 2XQBA 4YB9D 4Q65A 4NEJA 3DUHC 3UF2A 5EQGA 2ILKA 1Y1VD 1A22A 5FHXA 3PIVA 4IKZA 3DI2A 1AX8A 2O27A 3WCYI 5L6YC 2Q14A 1LQSL 3NCEA 4OAAA 4NI7A 1CYLA 3UX9A 1RCBA 5C65A 1EVSA 1M4RA 5D71A 1BGDA 1ITFA 5D6KA 2LMSA 4LRLA 1PV7A 4UVMA 4DKEA 4BY1D 1M4CA 1M4BA 5D59A 1A7MA 2JA6D 4IU8A 4A3DD 1M48A 1QVNA 4A3GD 3S9DA 1PV6A 2R93D 4WRLB 1ILKA 1NBPA 4A3ID 4NN6A 2B8XA 2LAGA 3H3VE 4A93D 5C3ED 1AXIA 2JA7D 3INKC 3I4MD 1PW4A 4JREA 5E4EA 4BBSD 4A3CD 3O7QA
chains in the Genus database with same CATH topology
5D28B 1JLIA 1F45B 2XQBA 3MZGA 4NKQC 1EKUA 2PSMA 5D22A 3OQ3A 3TGXB 3VA2A 4NEJA 2B8ZA 4YDYI 3HOVD 4GS7A 2GMFA 2CYKA 1EMRA 4Z5RD 3SE3B 1BBNA 4DOHA 4A3BD 3D48P 1GA3A 2D9QA 1RW5A 1CN4C 1HZIA 3DUHC 3EJJA 4A3MD 1WCMD 3QT2C 3PIWA 3UF2A 1HWHA 3NPZA 1Y6KL 2R92D 1ITIA 1M4AA 4DKDA 4EXNA 4PS4A 2ILKA 5IYCD 1Y1VD 1BUYA 1FG9A 2Z3RA 2VUMD 1B5LA 1IARA 1A22A 3N0PA 2HYMB 5FHXA 4ZS7A 3PO2D 1J7VL 3FKID 1P9MB 1BGEA 4RS1A 1I1RB 3OG4A 3PIVA 4A3FD 1PW6A 3LB6A 2OQPA 3DI2A 4DKFA 1AX8A 1Z7CA 3G6DA 2O27A 4EXPA 1INRA 3WCYI 5IP9D 1HWGA 1BGCA 1HULA 3DGCL 5D70A 4A3KD 4A3LD 1Y1WD 3HMXB 5TS9A 2B5IA 1ETEA 5L6YC 2Q14A 3UF5A 1LQSL 1Y6ML 3HOXD 3NCEA 5C44D 4NI7A 2KZ1A 1IK0A 2Q7NB 1ITMA 5FUCA 1CYLA 2B63D 2JA5D 1WU3I 1ALUA 1KF9A 3SE4B 3UX9A 1IJZA 1RCBA 5FLMD 2ERJD 4YQXA 4ZF7A 2L3YA 2L3OA 5C7XA 1D9GA 4O6KA 4YPGC 3HHRA 1GNCA 3NCBA 1HIJA 1N1FA 3BPOA 3AYHA 1EVSA 1M4RA 5D71A 1BGDA 5IP7D 4CNIC 4NN7A 1ITFA 2H24A 2LMSA 4X51A 1LKIA 4LRLA 2D48A 2O26A 5IYBD 3B5KA 3QB7A 3EW3A 1PGRA 2JA8D 3QWRB 5C4XD 1CD9A 1RHGA 1D9CA 1M47A 4DKEA 4A3JD 5D72A 4GRWA 4BY1D 1M4CA 1EERA 3I4ND 1IRLA 1M4BA 3HHCA 4BY7D 1ITLA 1A7MA 3DLQI 2B90A 4DKCA 4FA8E 2JA6D 3BPNA 3DI3A 1EXZA 1Y6NL 3HOUD 3HOYD 1HGUA 3NCFA 3OG6A 1HUWA 2R7ZD 4A3DD 1M48A 1QVNA 4A3GD 1IL6A 3HOZD 1VLKA 3S9DA 4YUEC 2B8YA 1CNT1 2Q98A 1YKBA 3IRHA 4O9HA 4A3ED 3BPLA 4WRLB 2R93D 3L5WI 4MHLA 1ILKA 1NBPA 4A3ID 2B8UA 4NN6A 1CSGA 1V7MV 2C35A 2B8XA 3BESL 2LAGA 4NEMA 5KNHI 3H0GD 4NI9A 3H3VE 3L5XA 1FYHA 3D85C 4J4LC 4A93D 1PVHB 5IYDD 5C3ED 1AXIA 1BP3A 1RFBA 1V7NV 3LB6B 2JA7D 3HOWD 1BCNA 1PY2A 3INKC 3N06A 4BBRD 3I4MD 3PO3D 5LQBA 2Z3QA 1LK3A 3D87A 4I77Z 2IL6A 3Q1SI 2O6IA 1Y14A 3G9VB 1AU1A 1Z92A 3NCCA 4NN5A 2E9WC 2B91A 1M49A 1SCFA 1HIKA 3QB1A 5E4EA 4BBSD 3QAZA 2INTA 3UEZE 4A3CD 4BXXD 1F6FA
chains in the Genus database with same CATH homology


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