4A3ID

Rna polymerase ii binary complex with dna
Total Genus 47
Loading diagram...

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


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

 
#similar chains in the Genus database (?% sequence similarity)
...loading similar chains, please wait...
#similar chains, but unknotted
...loading similar chains, please wait...
#similar chains in the pdb database (?% sequence similarity)
...loading similar chains, please wait...