3HOVD

Complete rna polymerase ii elongation complex ii
Total Genus 48
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
48
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
{{ tooltip.sname }} connected with {{ tooltip.tname }} : {{qFormat(tooltip.svalue) }}
molecule tags Transcription, transferase/dna/rna
molecule keywords DNA-directed RNA polymerase II subunit RPB1
publication title Structural basis of transcription: mismatch-specific fidelity mechanisms and paused RNA polymerase II with frayed RNA.
pubmed doi rcsb
total genus 48
structure length 178
sequence length 219
ec nomenclature
pdb deposition date 2009-06-03

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; 3hovD02
2R92D 2R7ZD 4A3GD 5C44D 4BY7D 1Y1VD 3HOUD 3FKID 2JA5D 3PO2D 5C4XD 3HOYD 2JA6D 2B63D 4A93D 4BBSD 2JA8D 3AYHA 3HOXD 3I4ND 3HOWD 2R93D 2JA7D 3H3VE 5IYBD 1Y1WD 4BBRD 3I4MD 5IYDD 4A3ID 4BXXD 3PO3D 5IP7D 3H0GD 5FLMD 3HOVD 5IYCD 4BY1D 4A3KD 4A3DD 2C35A 5IP9D 4A3CD 4A3JD 4A3BD 4A3ED 1WCMD 4A3MD 4A3LD 3HOZD 5C3ED 2VUMD 1Y14A 4A3FD
chains in the Genus database with same CATH superfamily
4PYPA 4NI7A 1AXIA 3BESL 3HOXD 2KZ1A 3OG4A 4ZWBA 1Y1WD 2XQBA 4EXNA 3N06A 1M48A 3HHCA 2C35A 1EERA 1ETEA 4A3LD 4ZYRA 3FKID 1BCNA 2R93D 4RS1A 4UVMA 4OH3A 4GBYA 4YQXA 3SE3B 5D72A 1HGUA 4I77Z 3D87A 4U4TA 1HIKA 2VUMD 1B5LA 5L6YC 1ILKA 4IKZA 3QAZA 1GNCA 1I1RB 5TS9A 4EXPA 4IKYA 1IK0A 4BY1D 5IP9D 4A3CD 5C3ED 3BPNA 1Y6KL 1D9CA 4XNJA 4BY7D 1RFBA 3IRHA 2ERJD 3L5XA 1NBPA 2CYKA 1FG9A 1N1FA 1SCFA 2JA7D 4DKEA 4DOHA 3UF2A 1YKBA 3NCFA 5D6KA 5IYDD 1BGDA 1PW6A 1VLKA 4JR9A 3BPLA 5A2OA 4FA8E 3HHRA 5D22A 3DGCL 2JA6D 4WRLB 3HOWD 1M47A 3BPOA 1ITFA 2Y5YA 3D48P 3QWRB 1M4CA 4A3JD 1P9MB 1Z92A 4A3FD 4X51A 1PW4A 2JA5D 2D9QA 3Q1SI 3NCBA 1F6FA 5D58A 3OG6A 2Q14A 4APSA 2PSMA 4TPHA 4J05A 5E4EA 4A3ED 1WCMD 1IJZA 1Y6ML 3HOUD 3HOYD 4DKCA 4D2CA 4NKQC 5GXBA 1M4RA 4TPGA 4LRLA 4NN7A 2INTA 4BXXD 1HWHA 3DI3A 1WU3I 4NEMA 1AX8A 1KF9A 4A3MD 4YB9D 1Y14A 3D85C 5EQHA 2O26A 3NCEA 1CN4C 3G9VB 3QT2C 1F45B 4GS7A 4LDSA 2JA8D 2O6IA 3LB6B 1CD9A 4Q65A 5IYBD 3HMXB 1M4AA 4LEPA 4D2DA 1Y6NL 3N0PA 4D2BA 3UF5A 2V8NA 2Q98A 4OAAA 2R7ZD 1EMRA 4A3GD 2H24A 3DLQI 3PIWA 1INRA 3O7PA 4IU9A 4BBSD 4IKXA 1LQSL 2HYMB 3O7QA 4YBQA 2O27A 2XUTA 4DKDA 2ILKA 4J4LC 5D59A 3TGXB 1HULA 2B5IA 1PVHB 4TPJA 1BP3A 4Z5RD 1EVSA 4DKFA 3PIVA 3H3VE 2B8XA 5IP7D 1JLIA 5FLMD 1PV6A 1V7NV 5A2NA 4ZF7A 5LQBA 1CNT1 3G6DA 1RCBA 1EKUA 2D48A 3SE4B 1IRLA 2B8YA 5EQGA 2Z3QA 5FUCA 1ITLA 4NN5A 4YPGC 4MHLA 1ALUA 3WCYI 1EXZA 1BGCA 1V7MV 3I4MD 4CNIC 4GRWA 3HOZD 1PV7A 1RHGA 5C44D 3S9DA 1HWGA 1Z7CA 2B91A 3INKC 2Z3RA 2B8ZA 3EJJA 3NCCA 1AU1A 3MZGA 3H0GD 4NEJA 4YDYI 4U4WA 4O9HA 3OQ3A 4IKVA 2L3YA 2B90A 1GA3A 5D28B 3PO2D 2E9WC 1D9GA 3WDOA 1BUYA 1IARA 3QB7A 5IYCD 3B5KA 4A3DD 3DUHC 1HZIA 3QB1A 3NPZA 4YUEC 1LKIA 2L3OA 1Y1VD 5C7XA 5C4XD 1HIJA 5EQIA 2LMSA 3AYHA 3L5WI 3I4ND 1CYLA 4IKWA 5C65A 4PS4A 4ZS7A 4BBRD 1HUWA 2Q7NB 3HOVD 2CFPA 4A3KD 2GMFA 5D70A 4A3BD 1ITMA 4W6VA 4NN6A 3UX9A 1A7MA 4XNIA 1M49A 2CFQA 3VA2A 2B63D 4A93D 1RW5A 4U4VA 1LK3A 5D71A 3UEZE 1M4BA 3PO3D 4A3ID 4QIQA 3LB6A 1J7VL 4ZW9A 1CSGA 2R92D 2OQPA 1BGEA 1ITIA 1PY2A 4ZWCA 1PGRA 1IL6A 4O6KA 2IL6A 2LAGA 5KNHI 3DI2A 4GC0A 4JA3A 1QVNA 2B8UA 4NI9A 5FHXA 1FYHA 4GBZA 3EW3A 4IU8A 1BBNA 1A22A 4JREA
chains in the Genus database with same CATH topology
2R7ZD 2L3YA 1EMRA 2B90A 3BPLA 4NI7A 4FA8E 4A3GD 2H24A 3DLQI 3PIWA 1GA3A 5D28B 3HHRA 1AXIA 3BESL 1INRA 3PO2D 5D22A 3DGCL 2E9WC 2JA6D 4BBSD 4WRLB 2KZ1A 1LQSL 3HOXD 3HOWD 1M47A 1D9GA 3BPOA 3OG4A 2HYMB 1BUYA 1Y1WD 1IARA 1ITFA 2O27A 3QB7A 2XQBA 4EXNA 3N06A 1M48A 5IYCD 3B5KA 3D48P 3HHCA 3QWRB 3DUHC 4DKDA 2ILKA 4J4LC 2C35A 4A3DD 1HZIA 1M4CA 1EERA 1P9MB 3QB1A 4A3JD 1ETEA 3TGXB 4A3LD 3NPZA 1Z92A 1HULA 2B5IA 1LKIA 4YUEC 4A3FD 1PVHB 4X51A 2L3OA 1Y1VD 5C7XA 3FKID 2JA5D 5C4XD 1HIJA 1BP3A 4Z5RD 1EVSA 2LMSA 2D9QA 3AYHA 3L5WI 3NCBA 3Q1SI 4DKFA 3I4ND 1BCNA 1F6FA 3PIVA 1CYLA 2R93D 3OG6A 2Q14A 3H3VE 4RS1A 4PS4A 4ZS7A 2B8XA 2PSMA 4BBRD 1HUWA 4YQXA 5IP7D 3SE3B 2Q7NB 1JLIA 5FLMD 5D72A 1V7NV 3HOVD 1HGUA 5E4EA 4I77Z 4A3KD 2GMFA 3D87A 4ZF7A 5D70A 5LQBA 1CNT1 4A3BD 3G6DA 4A3ED 1WCMD 1ITMA 4NN6A 1HIKA 1IJZA 3UX9A 1A7MA 1RCBA 1EKUA 1B5LA 2D48A 3SE4B 2VUMD 1IRLA 1Y6ML 2B8YA 5L6YC 1ILKA 2Z3QA 5FUCA 1ITLA 4NN5A 4YPGC 1M49A 3QAZA 3HOUD 1GNCA 1I1RB 3VA2A 3HOYD 2B63D 4MHLA 1ALUA 5TS9A 4DKCA 1RW5A 4EXPA 4A93D 4NKQC 1LK3A 3WCYI 1M4RA 5D71A 1EXZA 3UEZE 4LRLA 4NN7A 2INTA 1M4BA 1BGCA 1V7MV 3I4MD 4BXXD 4A3ID 1HWHA 3DI3A 4CNIC 3PO3D 1WU3I 1IK0A 4NEMA 4BY1D 4GRWA 5IP9D 4A3CD 1AX8A 3LB6A 1KF9A 4A3MD 3HOZD 5C3ED 1J7VL 3BPNA 1Y14A 3D85C 1Y6KL 1CSGA 1D9CA 1RHGA 2R92D 2OQPA 1BGEA 1ITIA 1PY2A 4BY7D 5C44D 1RFBA 3IRHA 2O26A 2ERJD 3NCEA 3L5XA 3S9DA 1PGRA 1IL6A 1CN4C 1NBPA 1HWGA 1Z7CA 1F45B 2CYKA 1FG9A 3G9VB 2B91A 3INKC 3QT2C 4GS7A 2JA8D 2O6IA 4O6KA 2Z3RA 1N1FA 3LB6B 1CD9A 1SCFA 2B8ZA 2IL6A 3EJJA 3NCCA 2JA7D 4DKEA 4DOHA 5IYBD 1AU1A 3UF2A 1YKBA 3HMXB 2LAGA 3NCFA 5KNHI 1M4AA 5IYDD 3DI2A 3MZGA 3H0GD 1BGDA 1Y6NL 1QVNA 2B8UA 4NEJA 4NI9A 5FHXA 1FYHA 1PW6A 3N0PA 4YDYI 1VLKA 3EW3A 3UF5A 1BBNA 2Q98A 1A22A 4O9HA 3OQ3A
chains in the Genus database with same CATH homology


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