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


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