4A3FD

Rna polymerase ii initial transcribing complex with a 6nt dna-rna hybrid and soaked with ampcpp
Total Genus 54
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
54
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) }}
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 54
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; 4a3fD02
5IYCD 2JA6D 4A3JD 3HOUD 3PO3D 4A3BD 1Y1WD 3HOXD 4A3ID 4A3LD 5C4XD 3I4MD 4BBRD 2B63D 4BXXD 4A3CD 2VUMD 3I4ND 3PO2D 1Y14A 4BBSD 2R7ZD 3FKID 2JA7D 4A3MD 4A93D 2JA8D 5IYDD 1WCMD 3HOVD 3HOWD 5IYBD 2R93D 4BY7D 2R92D 2JA5D 2C35A 4A3ED 4A3GD 5IP9D 3AYHA 5C3ED 4A3KD 3HOZD 4BY1D 3H3VE 3H0GD 3HOYD 5IP7D 5FLMD 4A3FD 4A3DD 1Y1VD 5C44D
chains in the Genus database with same CATH superfamily
1F45B 1Y6KL 1B5LA 4NEMA 1BGDA 4DKDA 1A22A 4A3MD 5A2NA 4J05A 4BY7D 1M4RA 5IP9D 4CNIC 1PW6A 4U4TA 3IRHA 2CFQA 3BPNA 4MHLA 4U4VA 4NI7A 1ITIA 1P9MB 4X51A 1HWHA 1WCMD 4ZWBA 4YUEC 1AU1A 1VLKA 3EJJA 4O6KA 2KZ1A 5TS9A 5C44D 3HHCA 3N0PA 2LMSA 5C4XD 5A2OA 3UX9A 1HIJA 3D87A 1EVSA 1D9CA 1ALUA 5C65A 2B8ZA 3HOVD 1NBPA 3PIVA 2C35A 3LB6B 4A3ED 2V8NA 4YQXA 1RFBA 3QAZA 3MZGA 1IJZA 2XQBA 1CYLA 2L3OA 2D48A 4YDYI 4A3ID 2B63D 4BBRD 3I4ND 4FA8E 4I77Z 1ITFA 4UVMA 4IKVA 4NN5A 2JA5D 1IL6A 3HMXB 5D22A 1BP3A 2Y5YA 1RCBA 3D48P 4GC0A 3HOXD 2H24A 4NN7A 1PW4A 1I1RB 3S9DA 1HGUA 1M4AA 5KNHI 1JLIA 3SE4B 4Q65A 4DOHA 1IK0A 1KF9A 5D72A 1EXZA 4QIQA 3EW3A 2IL6A 3NCBA 4U4WA 1ITMA 4A3CD 4ZW9A 1WU3I 4DKCA 1V7MV 4OH3A 5D70A 4A3FD 1AX8A 1CD9A 1ITLA 1EMRA 1IRLA 1D9GA 1Y1WD 3DI3A 3D85C 4BXXD 1HULA 4NI9A 1BBNA 2B8YA 4IKWA 4DKEA 1M47A 1HUWA 3BPOA 4GBYA 2B8XA 2PSMA 5IYDD 1J7VL 1M48A 4TPGA 2O27A 4A3BD 4JR9A 3SE3B 5FHXA 3DI2A 5EQHA 5E4EA 4A93D 2B5IA 5IYBD 2R92D 2D9QA 4GBZA 5C3ED 1PY2A 4JA3A 3N06A 3WCYI 3H0GD 4PS4A 5L6YC 3I4MD 1BGCA 2Q14A 3PO2D 3OG6A 4J4LC 3O7PA 2XUTA 1RW5A 4ZWCA 1GNCA 3NCFA 4YB9D 3H3VE 1AXIA 4D2DA 5D59A 1CSGA 3O7QA 3VA2A 4TPHA 2B90A 4A3LD 4WRLB 1QVNA 3NPZA 3B5KA 3WDOA 2JA8D 3L5WI 4APSA 4IKZA 5GXBA 4D2CA 3HOZD 1GA3A 4OAAA 5EQGA 4EXNA 2O26A 4Z5RD 4NKQC 5D28B 4ZYRA 2L3YA 1SCFA 3UF2A 3L5XA 2VUMD 4NEJA 5EQIA 3G6DA 3LB6A 3TGXB 1PV7A 3QB7A 5D58A 4BY1D 1CNT1 3DLQI 4ZS7A 1BUYA 4IKYA 1RHGA 3QB1A 5C7XA 2Z3RA 1ILKA 4A3JD 4TPJA 3PO3D 1IARA 4GRWA 1PVHB 3DGCL 3QT2C 1Y14A 1HIKA 3FKID 2JA7D 4GS7A 1Y6NL 1Z7CA 3HOWD 5LQBA 1LQSL 4NN6A 3AYHA 4IU8A 2GMFA 4A3DD 1Z92A 1HWGA 3OQ3A 5IYCD 3HOUD 4LEPA 4PYPA 2OQPA 1Y6ML 2HYMB 3NCEA 1FYHA 4LRLA 3G9VB 5D6KA 1EKUA 3UF5A 3INKC 4DKFA 1N1FA 3Q1SI 4O9HA 2CYKA 4EXPA 1V7NV 1CN4C 3HHRA 3DUHC 2JA6D 1EERA 2B8UA 4JREA 4W6VA 1BGEA 5FUCA 3QWRB 1M49A 2R7ZD 4YBQA 1LKIA 3NCCA 1FG9A 4A3KD 4RS1A 1YKBA 1HZIA 4IU9A 1Y1VD 2O6IA 1INRA 3UEZE 1PV6A 1PGRA 2Z3QA 2INTA 2CFPA 5D71A 2E9WC 2Q7NB 1F6FA 2R93D 1ETEA 1M4CA 3PIWA 1A7MA 2LAGA 5FLMD 1M4BA 4XNJA 2B91A 4XNIA 1BCNA 3OG4A 3BESL 1LK3A 4IKXA 4D2BA 4YPGC 3BPLA 2Q98A 4BBSD 4ZF7A 4LDSA 2ILKA 4A3GD 2ERJD 3HOYD 5IP7D
chains in the Genus database with same CATH topology
5IYCD 1RCBA 1F45B 3D48P 1Y6KL 3HOUD 1B5LA 4NEMA 3HOXD 4PS4A 5L6YC 2OQPA 3I4MD 1BGCA 2H24A 2Q14A 4NN7A 1BGDA 1Y6ML 2HYMB 3NCEA 1FYHA 3PO2D 1I1RB 4DKDA 3S9DA 3OG6A 4J4LC 4LRLA 1A22A 3G9VB 4A3MD 1RW5A 1HGUA 1EKUA 4BY7D 1GNCA 3UF5A 1M4RA 5IP9D 3INKC 1M4AA 4CNIC 1JLIA 1N1FA 3NCFA 4DKFA 1PW6A 5KNHI 3Q1SI 3IRHA 3H3VE 3SE4B 4O9HA 2CYKA 4DOHA 4EXPA 1IK0A 1AXIA 1CN4C 1V7NV 3BPNA 1KF9A 5D72A 1CSGA 1EXZA 3HHRA 3DUHC 3VA2A 2JA6D 4MHLA 1EERA 2B90A 4NI7A 2B8UA 3EW3A 2IL6A 4A3LD 3NCBA 4WRLB 1ITMA 1ITIA 1BGEA 5FUCA 4A3CD 3QWRB 1QVNA 3NPZA 1M49A 1P9MB 2R7ZD 3B5KA 4X51A 1HWHA 1LKIA 2JA8D 1WCMD 3L5WI 4YUEC 1AU1A 3NCCA 1WU3I 1FG9A 1VLKA 4DKCA 3EJJA 1V7MV 4O6KA 4A3KD 3HOZD 4RS1A 5D70A 1GA3A 1YKBA 4A3FD 1AX8A 2KZ1A 4EXNA 1HZIA 1Y1VD 5TS9A 1CD9A 5C44D 1ITLA 1EMRA 2O26A 1IRLA 2O6IA 1INRA 1D9GA 3HHCA 4NKQC 4Z5RD 3N0PA 5D28B 1PGRA 3UEZE 2L3YA 1Y1WD 2LMSA 3DI3A 2Z3QA 1SCFA 5C4XD 3UF2A 2INTA 3D85C 3L5XA 3UX9A 1HULA 4BXXD 1HIJA 5D71A 4NI9A 2VUMD 3D87A 1EVSA 1D9CA 2E9WC 4NEJA 1BBNA 2Q7NB 1ALUA 3G6DA 2B8YA 3LB6A 2B8ZA 3HOVD 1NBPA 1F6FA 3TGXB 3PIVA 4DKEA 1M47A 2R93D 1ETEA 2C35A 3LB6B 1M4CA 1HUWA 3QB7A 3PIWA 4A3ED 1A7MA 3BPOA 4YQXA 4BY1D 1CNT1 3DLQI 2LAGA 1M4BA 1RFBA 1BUYA 4ZS7A 1RHGA 2B91A 3QB1A 3QAZA 5FLMD 3MZGA 2B8XA 1BCNA 3OG4A 3BESL 5C7XA 1IJZA 2XQBA 2PSMA 5IYDD 2L3OA 1J7VL 1CYLA 1LK3A 2Z3RA 1M48A 1ILKA 2D48A 4YDYI 4A3JD 2O27A 3PO3D 1IARA 4A3BD 4GRWA 4A3ID 4YPGC 3BPLA 3SE3B 4BBRD 2B63D 1PVHB 5FHXA 3I4ND 3DI2A 4FA8E 3DGCL 2Q98A 1Y14A 3QT2C 5E4EA 4BBSD 4ZF7A 1HIKA 3FKID 4I77Z 2JA7D 4A93D 4GS7A 1Y6NL 1Z7CA 3HOWD 1ITFA 5LQBA 1LQSL 2ILKA 2B5IA 4NN6A 4NN5A 5IYBD 2R92D 2JA5D 4A3GD 2D9QA 2ERJD 3AYHA 1IL6A 5C3ED 2GMFA 1PY2A 3N06A 3WCYI 3H0GD 3HOYD 5IP7D 3HMXB 4A3DD 1Z92A 5D22A 1HWGA 3OQ3A 1BP3A
chains in the Genus database with same CATH homology


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