4A3GD

Rna polymerase ii initial transcribing complex with a 2nt dna-rna hybrid
Total Genus 52
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
52
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
molecule keywords DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1
publication title Structural basis of initial RNA polymerase II transcription.
pubmed doi rcsb
total genus 52
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; 4a3gD02
2JA5D 4A3ED 3HOZD 4BBSD 5IYDD 4BXXD 2JA8D 2R92D 4A93D 4BY1D 4BBRD 3PO3D 4A3ID 1Y1WD 1WCMD 2VUMD 2R7ZD 5IP7D 4A3KD 4A3MD 4A3BD 4BY7D 3HOXD 4A3LD 5IYBD 2C35A 3H3VE 5FLMD 3HOWD 1Y14A 5IP9D 3HOUD 4A3DD 4A3GD 3HOVD 2B63D 3PO2D 5IYCD 3I4ND 5C3ED 2JA6D 1Y1VD 3I4MD 4A3JD 4A3CD 2R93D 3H0GD 5C4XD 5C44D 2JA7D 3FKID 3AYHA 4A3FD 3HOYD
chains in the Genus database with same CATH superfamily
4PS4A 2JA5D 3EJJA 1Z7CA 1GA3A 4IKYA 1WCMD 2B8ZA 2Y5YA 5E4EA 5IP9D 3HOVD 1BGCA 3SE3B 5EQIA 3BPLA 3WDOA 5C4XD 1HIKA 4ZW9A 1ITIA 5C7XA 4RS1A 2LMSA 1LKIA 4IKVA 4TPGA 4NEMA 4BY7D 1RFBA 2HYMB 5D58A 1V7MV 3LB6B 1RHGA 4LRLA 5EQHA 3QWRB 4PYPA 4YUEC 1M48A 4IU9A 5IYDD 4LDSA 3QT2C 4J4LC 1BBNA 3B5KA 4A3DD 3HOWD 1HUWA 1N1FA 4GRWA 4TPJA 1PY2A 2D48A 5C3ED 4ZWBA 4OH3A 1IL6A 5D72A 1ILKA 3BPOA 3PO3D 1HIJA 1IARA 3NCEA 4X51A 3DGCL 1M4CA 4A93D 4A3KD 2XUTA 1PGRA 1NBPA 3MZGA 4U4VA 1ITLA 3H0GD 4NI7A 5D59A 2E9WC 4APSA 4GBZA 3D48P 4ZWCA 4GC0A 1BCNA 3UF2A 3DI3A 3N06A 4DKFA 2VUMD 1Y1WD 2R7ZD 3NCFA 2V8NA 1EKUA 1Y6KL 2JA6D 1CYLA 3S9DA 1BP3A 1ITFA 5D22A 4YB9D 2B63D 2B8YA 4DOHA 1PW6A 3EW3A 4LEPA 1QVNA 1BGDA 4GBYA 4O6KA 2B5IA 2OQPA 2CFQA 1Y14A 4MHLA 3G9VB 3PO2D 1A22A 2O27A 3DI2A 5D71A 4D2BA 4I77Z 1M4RA 3O7PA 3AYHA 5A2OA 5FHXA 1FG9A 3INKC 4TPHA 4DKDA 4XNJA 4NN7A 2Q14A 1HGUA 4D2DA 4J05A 5IYBD 1M4AA 3HOUD 1PV6A 3BPNA 1EERA 2R93D 1D9CA 4GS7A 4IU8A 2B90A 1RCBA 1KF9A 4FA8E 3UEZE 4WRLB 3DUHC 3NCBA 4IKWA 1INRA 1B5LA 5TS9A 4NN5A 3PIVA 2INTA 5C65A 3OG6A 2IL6A 1RW5A 2Z3RA 1A7MA 4A3ED 1IK0A 4JREA 2H24A 1F6FA 5IP7D 4A3LD 1Z92A 3G6DA 4DKEA 1HWGA 1EXZA 3I4MD 1I1RB 3TGXB 3FKID 1F45B 2Q7NB 1EMRA 1AX8A 3HOZD 4JR9A 4BXXD 1HWHA 1IJZA 2Q98A 1CNT1 2CFPA 3NCCA 2B8UA 4CNIC 4U4WA 4NKQC 4XNIA 1ITMA 2B91A 4IKZA 1HZIA 1LQSL 1M4BA 1YKBA 5D28B 4NN6A 1AU1A 3VA2A 4Q65A 1ETEA 4A3GD 4YQXA 4D2CA 1M47A 4ZF7A 4JA3A 2O6IA 4BBSD 2Z3QA 3WCYI 2PSMA 3D87A 4BBRD 4A3ID 1J7VL 4A3BD 3O7QA 3HOXD 5A2NA 5KNHI 1EVSA 3UX9A 5L6YC 1GNCA 3QAZA 4YPGC 4A3CD 3PIWA 5FUCA 2B8XA 3N0PA 3DLQI 4EXPA 5D70A 1JLIA 4DKCA 2ERJD 4YBQA 2R92D 2XQBA 4BY1D 2ILKA 4YDYI 4A3MD 1CN4C 3QB7A 3NPZA 3HHRA 3OQ3A 1Y1VD 4O9HA 5EQGA 2JA7D 4IKXA 1IRLA 5LQBA 1CSGA 1PV7A 2JA8D 3Q1SI 1WU3I 1VLKA 4QIQA 3H3VE 1BGEA 3LB6A 3QB1A 5IYCD 3I4ND 3HMXB 4A3JD 1LK3A 4Z5RD 3OG4A 1M49A 3HOYD 4U4TA 4NI9A 2CYKA 1BUYA 4ZYRA 3L5WI 1PW4A 1V7NV 1Y6ML 2L3OA 3HHCA 1AXIA 1HULA 1Y6NL 1P9MB 2L3YA 4ZS7A 1CD9A 3SE4B 5GXBA 3D85C 1SCFA 3UF5A 2LAGA 4W6VA 1PVHB 4OAAA 2C35A 1ALUA 5FLMD 4EXNA 3L5XA 4NEJA 2GMFA 1D9GA 3BESL 5D6KA 3IRHA 4UVMA 5C44D 2O26A 1FYHA 2KZ1A 4A3FD 2D9QA
chains in the Genus database with same CATH topology
4PS4A 2JA5D 3EJJA 4A3ED 3D48P 3DLQI 4EXPA 5D70A 1BCNA 1JLIA 3DI3A 3N06A 3UF2A 4DKCA 2ERJD 1IK0A 1Z7CA 4DKFA 2R92D 2H24A 1GA3A 2XQBA 4BY1D 2ILKA 4YDYI 1F6FA 2VUMD 1Y1WD 1WCMD 2B8ZA 2R7ZD 5IP7D 4A3MD 1CN4C 3NCFA 4A3LD 5E4EA 3PO3D 3QB7A 1Z92A 5IP9D 3HOVD 1BGCA 3NPZA 3G6DA 3SE3B 1HWGA 1EKUA 4DKEA 1Y6KL 3HHRA 2JA6D 1CYLA 3OQ3A 3S9DA 1BP3A 1Y1VD 1EXZA 3BPLA 4O9HA 3I4MD 1I1RB 5C4XD 5D22A 1ITFA 2JA7D 3TGXB 3FKID 1HIKA 1ITIA 1F45B 2Q7NB 1IRLA 1EMRA 2B63D 2B8YA 1AX8A 5C7XA 3HOZD 4DOHA 5LQBA 4RS1A 1PW6A 1CSGA 4BXXD 1HWHA 3EW3A 2LMSA 2JA8D 1QVNA 1IJZA 1LKIA 3Q1SI 1WU3I 1VLKA 4NEMA 1BGDA 4BY7D 4O6KA 2Q98A 2B5IA 2OQPA 3H3VE 1BGEA 3LB6A 1Y14A 3QB1A 4MHLA 1RFBA 3G9VB 1CNT1 3PO2D 2HYMB 3NCCA 2B8UA 5IYCD 1A22A 3I4ND 4CNIC 3HMXB 4NKQC 4A3JD 2O27A 3DI2A 5D71A 1LK3A 1V7MV 4I77Z 4Z5RD 3LB6B 1M4RA 1RHGA 4LRLA 3OG4A 3QWRB 3AYHA 1M49A 1ITMA 3HOYD 4YUEC 2B91A 1M48A 5FHXA 1FG9A 1HZIA 3INKC 1LQSL 4DKDA 5IYDD 2CYKA 4NI9A 1M4BA 3QT2C 1YKBA 4J4LC 5D28B 4NN6A 1BBNA 1AU1A 3B5KA 1BUYA 4NN7A 2Q14A 1HGUA 3VA2A 5IYBD 4A3DD 1ETEA 3HOWD 1M4AA 3HOUD 1HUWA 3L5WI 4EXNA 4A3GD 1N1FA 1V7NV 4YQXA 4GRWA 1PY2A 2D48A 5C3ED 1Y6ML 2L3OA 2KZ1A 3BPNA 1EERA 3HHCA 1AXIA 1M47A 2R93D 1D9CA 4ZF7A 1HULA 1Y6NL 1IL6A 4GS7A 1P9MB 5D72A 2O6IA 1ILKA 2B90A 2L3YA 1HIJA 1IARA 3BPOA 3NCEA 1CD9A 4X51A 4ZS7A 2Z3QA 3DGCL 3WCYI 4BBSD 1RCBA 1KF9A 3SE4B 2PSMA 4FA8E 1M4CA 3D85C 4WRLB 3UEZE 4A93D 3DUHC 3NCBA 3D87A 1SCFA 3UF5A 4BBRD 2LAGA 4A3ID 1J7VL 4A3KD 1INRA 1B5LA 4A3BD 1PVHB 3HOXD 5KNHI 2C35A 1ALUA 5TS9A 5FLMD 1EVSA 3L5XA 4NEJA 4NN5A 2GMFA 1D9GA 1PGRA 2INTA 1NBPA 3PIVA 3UX9A 5L6YC 3MZGA 1ITLA 3OG6A 1GNCA 3BESL 3QAZA 2IL6A 3IRHA 4YPGC 3H0GD 4NI7A 4A3CD 1RW5A 3PIWA 2O26A 5C44D 2E9WC 1FYHA 5FUCA 2Z3RA 2B8XA 1A7MA 3N0PA 4A3FD 2D9QA
chains in the Genus database with same CATH homology


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