3HOZD

Complete rna polymerase ii elongation complex iv with a t-u mismatch and a frayed rna 3'-guanine
Total Genus 42
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
42
sequence length
219
structure length
179
Chain Sequence
VSTSTFQTRRRRLKKVEEEENAATLQLGQEFQLKQINHQGEEEELIALNLSEARLVIKEALVERRRAFKRSQKKETREKELESIDVLLEQTTGGNNKDLKNTMQYLTNFSRFRDQETVGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLNNKISDDELERILKELSNLETLY
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 hybrid
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 42
structure length 179
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; 3hozD02
5C44D 4A3GD 2R7ZD 2JA5D 4A3BD 5FLMD 5IYCD 4BY1D 5C4XD 2JA6D 4A3ID 4A3CD 3HOZD 2B63D 3PO3D 3PO2D 2C35A 1Y14A 3HOUD 4A3ED 2VUMD 4A3JD 2R93D 1WCMD 4A3MD 4A3LD 3HOWD 3HOXD 2JA8D 5C3ED 3HOYD 3AYHA 1Y1VD 4A3KD 4A3FD 5IP7D 5IYDD 4BY7D 4A93D 3H0GD 3FKID 2R92D 5IYBD 3H3VE 4BBRD 1Y1WD 3I4ND 4BXXD 3I4MD 4BBSD 4A3DD 3HOVD 5IP9D 2JA7D
chains in the Genus database with same CATH superfamily
4I77Z 1Z7CA 5IYCD 1AXIA 1FYHA 4A3CD 2LAGA 1LK3A 2Q98A 1GA3A 5FUCA 4TPJA 4ZYRA 3INKC 2INTA 4D2CA 1Y1VD 5A2OA 1M4BA 3H0GD 1RHGA 4JR9A 4GC0A 3WCYI 5FHXA 4APSA 4A3BD 1RCBA 1BP3A 2JA6D 1ITIA 1EVSA 5D58A 1BGDA 4Z5RD 4NN6A 1IK0A 3HOUD 4A3ED 2VUMD 4IKXA 1CNT1 1KF9A 1Y6ML 2B8YA 2B90A 1EERA 2D48A 4BXXD 5D6KA 4QIQA 4U4WA 1HIJA 4A3DD 5L6YC 4PYPA 4GBZA 3D85C 1IRLA 1I1RB 3UX9A 3UF2A 3TGXB 2H24A 5D70A 2B8ZA 5LQBA 4MHLA 3FKID 2R92D 2Z3RA 1ITFA 3I4MD 2B63D 4D2DA 1M4RA 2KZ1A 3DI3A 5D59A 1VLKA 4NKQC 4YBQA 2O6IA 1Y14A 4JREA 4NI7A 1D9GA 3S9DA 3DI2A 2E9WC 3OG6A 3I4ND 1V7NV 1PY2A 4LRLA 1EKUA 1QVNA 4YUEC 3SE4B 4BY1D 2L3OA 4NI9A 5GXBA 4IKVA 4A3ID 4XNJA 2R93D 1NBPA 3LB6A 4A3MD 1EXZA 3DGCL 4A3FD 5IP7D 4A93D 3O7QA 1HWHA 4J4LC 3UEZE 3H3VE 5IYBD 5D72A 3QB1A 5C7XA 1D9CA 1BBNA 4LEPA 3NCFA 1ITLA 1ILKA 1CN4C 4IKYA 3QB7A 2XUTA 1M4CA 4NEMA 2OQPA 3HMXB 1M49A 1PGRA 4XNIA 3QAZA 1PV6A 4ZF7A 3HHRA 2R7ZD 3N0PA 4YDYI 5C4XD 4DKCA 4DKDA 1F6FA 1HGUA 3EJJA 4X51A 3DUHC 3LB6B 4UVMA 4BBRD 1ALUA 4GRWA 5E4EA 2CFQA 3QT2C 4ZWBA 1JLIA 1BUYA 3PO2D 1Y6NL 4JA3A 2ERJD 5D28B 2Y5YA 1IJZA 4DKEA 3HHCA 1A22A 5IYDD 4BY7D 2ILKA 1INRA 3DLQI 1Y1WD 3PIVA 3HOVD 1ITMA 1AU1A 4O6KA 4YB9D 4J05A 4O9HA 1Y6KL 1M48A 3BPLA 1PVHB 4YPGC 1HIKA 3BPNA 5KNHI 4ZW9A 1HZIA 4EXPA 4D2BA 1BGEA 4OAAA 4A3GD 3D48P 4WRLB 4U4TA 1RFBA 3L5XA 3MZGA 2CFPA 4A3JD 1HUWA 3QWRB 3G9VB 1AX8A 1BGCA 2XQBA 5D22A 3HOZD 2JA7D 5C44D 4YQXA 4OH3A 1CSGA 5FLMD 1LQSL 2B91A 1PW4A 1BCNA 3OG4A 2D9QA 2HYMB 3AYHA 3NCCA 4IU9A 1IARA 1Z92A 1M4AA 3UF5A 4LDSA 1J7VL 3Q1SI 2L3YA 4BBSD 2JA5D 4IU8A 4ZWCA 4TPHA 3VA2A 3D87A 3OQ3A 4PS4A 1CYLA 4NEJA 3WDOA 2Z3QA 4A3LD 3HOXD 4DKFA 1GNCA 3HOYD 1WU3I 1LKIA 3SE3B 3PIWA 3G6DA 1SCFA 1B5LA 5A2NA 4ZS7A 3BESL 4Q65A 3EW3A 3B5KA 2B5IA 1WCMD 3L5WI 1V7MV 2B8XA 4RS1A 4GS7A 2GMFA 4CNIC 5IP9D 3NCBA 3NPZA 3PO3D 1ETEA 5C65A 4GBYA 2B8UA 1CD9A 5D71A 4EXNA 2CYKA 5EQIA 5EQGA 1FG9A 1HULA 5EQHA 2O26A 2Q7NB 3N06A 4IKWA 2O27A 2IL6A 1N1FA 1HWGA 2C35A 3BPOA 4TPGA 1RW5A 1PV7A 2Q14A 5C3ED 4NN5A 1YKBA 4U4VA 1IL6A 3IRHA 3NCEA 5TS9A 4W6VA 2V8NA 1M47A 1P9MB 1A7MA 2LMSA 3O7PA 4NN7A 3HOWD 1EMRA 2JA8D 4FA8E 4A3KD 1F45B 2PSMA 4IKZA 1PW6A 4DOHA
chains in the Genus database with same CATH topology
1AU1A 1B5LA 4O6KA 4I77Z 3SE4B 1Z7CA 3HOVD 5IYCD 4BY1D 1AXIA 1FYHA 2L3OA 3BESL 4O9HA 4ZS7A 4A3ID 1Y6KL 2LAGA 4NI9A 4A3CD 1M48A 1LK3A 2Q98A 3BPLA 1PVHB 1GA3A 5FUCA 3EW3A 3B5KA 4YPGC 2R93D 1NBPA 2B5IA 3LB6A 1WCMD 3L5WI 1EXZA 4A3MD 1HIKA 3BPNA 3DGCL 3INKC 5KNHI 2INTA 1V7MV 2B8XA 4RS1A 1Y1VD 4A3FD 5IP7D 4A93D 1M4BA 1HWHA 3H0GD 4GS7A 4J4LC 1HZIA 3UEZE 5IYBD 1RHGA 3H3VE 2GMFA 5D72A 3QB1A 5C7XA 1D9CA 4EXPA 4CNIC 1BBNA 1BGEA 5IP9D 4A3GD 3WCYI 3D48P 3NCFA 4WRLB 1ITLA 5FHXA 4A3BD 1ILKA 1CN4C 1RCBA 1BP3A 3NCBA 2JA6D 1ITIA 1EVSA 1BGDA 3NPZA 3PO3D 1RFBA 4Z5RD 3L5XA 4NN6A 1ETEA 1IK0A 3MZGA 2B8UA 3HOUD 4A3ED 2VUMD 1CD9A 4A3JD 3QB7A 1HUWA 5D71A 4EXNA 1M4CA 4NEMA 2CYKA 2OQPA 3HMXB 1CNT1 1KF9A 1FG9A 3QWRB 1HULA 1Y6ML 2B8YA 1M49A 3G9VB 2B90A 1PGRA 2O26A 1EERA 1AX8A 2D48A 1BGCA 4BXXD 3QAZA 2XQBA 1HIJA 5D22A 5L6YC 4A3DD 4ZF7A 3HOZD 2JA7D 2Q7NB 3HHRA 5C44D 3N06A 2R7ZD 2O27A 4YQXA 3N0PA 1CSGA 4YDYI 5FLMD 5C4XD 2IL6A 3D85C 1LQSL 1IRLA 1I1RB 1N1FA 3UX9A 4DKCA 3UF2A 1HWGA 2C35A 2B91A 3BPOA 1BCNA 1RW5A 4DKDA 1F6FA 3TGXB 2H24A 2Q14A 5C3ED 3OG4A 2D9QA 1HGUA 2HYMB 3EJJA 3AYHA 4X51A 5D70A 4NN5A 3DUHC 3NCCA 1YKBA 1IARA 3LB6B 1Z92A 2B8ZA 1M4AA 3UF5A 5LQBA 1IL6A 4MHLA 1J7VL 3FKID 3IRHA 3NCEA 3Q1SI 4BBRD 2Z3RA 2R92D 2L3YA 1ALUA 5TS9A 1ITFA 3I4MD 2B63D 4BBSD 1M4RA 4GRWA 2JA5D 1M47A 1P9MB 5E4EA 3QT2C 1A7MA 3VA2A 2KZ1A 1JLIA 3DI3A 1VLKA 4NKQC 3D87A 3OQ3A 1BUYA 2LMSA 2O6IA 4PS4A 3PO2D 1CYLA 4NEJA 1Y14A 1Y6NL 4NN7A 5D28B 2ERJD 2Z3QA 4A3LD 3HOWD 3HOXD 4DKFA 1EMRA 4NI7A 1D9GA 1IJZA 3S9DA 4DKEA 2JA8D 3DI2A 3HOYD 4FA8E 1GNCA 2E9WC 3HHCA 4A3KD 1A22A 5IYDD 1F45B 1WU3I 4BY7D 2ILKA 2PSMA 1LKIA 3OG6A 1PW6A 3SE3B 1INRA 3DLQI 1V7NV 1PY2A 1Y1WD 3I4ND 4DOHA 3PIWA 3PIVA 1EKUA 4LRLA 3G6DA 1SCFA 1QVNA 4YUEC 1ITMA
chains in the Genus database with same CATH homology


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