5JVH1

The crystal structure large ribosomal subunit (50s) of deinococcus radiodurans in complex with evernimicin
Total Genus 3
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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
3
sequence length
53
structure length
53
Chain Sequence
AKDGPRIIVKMESSAGTGFYYTTTKNRRNTQAKLELKKYDPVAKKHVVFREKK
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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
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molecule tags Ribosome
publication title Avilamycin and evernimicin induce structural changes in rProteins uL16 and CTC that enhance the inhibition of A-site tRNA binding.
pubmed doi rcsb
molecule keywords 23S ribosomal RNA
total genus 3
structure length 53
sequence length 53
ec nomenclature
pdb deposition date 2016-05-11

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
1 PF00471 Ribosomal_L33 Ribosomal protein L33
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
2.20.28.120 Mainly Beta Single Sheet Rubrerythrin, domain 2 Rubrerythrin, domain 2 5jvh100
5GAEc 4WFN1 5DM71 3PIO1 4UY81 5GAGc 5GAHc 5GADc 3J7Z1 5JVH1 4V196 3PIP1 5DM61 3J7Y1 4U671 5H1Sc 5JVG1 5MLC3
chains in the Genus database with same CATH superfamily
4WFN1 1SFOL 1S30A 4POGA 4BBSL 3I4NL 4TPUA 2JA6L 1VCXA 1OWBA 1TWCL 4JADA 1P7PA 1CADA 3LWOB 2E2HL 1I3QL 4A3KL 2CKCA 2VL6A 5EIOC 4A93L 1H7VA 5H1Sc 1FHHA 1DX8A 2PMZP 3KYVA 4POFA 2C6AA 4A3DL 4X6AL 2JA5L 1B13A 3RZ6A 1R0IA 2HVYC 1QYBA 1NXEA 1TWGL 1YUXA 2VUML 3HKZP 1IRNA 5FJ8L 2NVYL 5JVH1 1ZRPA 2PPTA 3MPSA 2J9UB 5M3FL 3GTPL 1NNQA 2EY4E 3KYYA 2CKAA 4A3JL 5MFPA 4U671 1RYQA 2ERJA 3MQKB 1F4LA 5M5XL 2ERSA 3GTLL 1RDGA 1YV1A 3HAXC 1LKMA 3B0AB 3HOVL 5C44L 3LWRB 3S1ML 3H3VM 2QL0A 2NVXL 2AUSB 2Z3RB 3SS2A 5M5WL 2C6BA 2M6OA 4AI2A 3S16L 3GTKL 1BE7A 3S17L 2M6PA 2R92L 3FDJA 3A44A 8RXNA 4A3LL 1B2JA 1NXGA 3H99A 3S14L 4BBRL 3PO2L 2PVEA 1JYBA 5MGNA 4A3EL 5M5YL 4C3JL 3QVDA 3B08B 5IYBL 2XJUA 1BQ9A 2LCQA 2A68D 3RYGA 4AR3A 3KYXA 4BY7L 6RXNA 1QQTA 3KYUA 2AQCA 2ZIXA 3GTOL 5GAEc 3P8BA 2XJPA 4YWMA 1RYTA 1S24A 2A6ED 3LPEB 2KN9A 1R0FA 1TWFL 1CAAA 2XJRA 1PFVA 2PSMC 4A3IL 3IU3I 5MF6A 3RZTA 1PFWA 1LKPA 4ZN3B 2M4YA 4B8CD 3HOYL 3S1NL 3M3YL 2WB1P 2L0ZA 4A3GL 3J7Z1 5DM61 3HOZL 4JAGA 3HOXL 3RZDL 2NVTL 4AR6A 5RXNA 4G6BA 3LWQB 1RB9A 2K2DA 2NVQL 4AI3A 1IROA 5AI3A 3S1RL 5IYCL 2B5ID 3LWPB 3PKIA 5AI2A 1SMUA 1PFUA 2Z3QB 3I4ML 2R7ZL 1I50L 1I6HL 3K35A 5DM71 2H12A 1T9PA 4C3HL 1Y1VL 4JAEA 4ME3A 2JI2A 2V3BB 4RXNA 3H97A 5EINC 2NYDA 4LHNA 5C4JL 2R93L 2M4VA 1YUZA 1SMWA 2E2IL 3PIO1 1WCML 1RWDA 2XJQA 5AN9H 1C09A 1QCVA 4AHZA 5IP9L 2JA8L 1SMMA 7RXNA 4AHYA 4A3CL 1ODHA 4Y52L 4A3BL 3FKIL 4AI0A 1R9TL 2XJSA 2XJTA 1S2ZA 3PIP1 3HJYB 1VZHA 4A3ML 1E8JA 1Z92B 4C2M1 5C3EL 5IYDL 2XJVA 2V0FA 1YK4A 1RDVA 5FLML 2RDVA 1BFYA 4YWLA 4C3IL 3WWLA 3H9CA 3M4OL 1BQ8A 1TWAL 4XGHA 4AI1A 3S2DL 1VZIA 5IP7L 4LHLA 2O5JD 1PZXA 3S2HL 2JI1A 1TWHL 4GS7D 1R0GA 1B71A 1IU6A 2KKDA 4TVMA 2JA7L 1VZGA 3GTGL 3RZOL 4Y7NL 3ZG6A 1OWCA 5GADc 2MS3A 1BRFA 4AHXA 3GTQL 4AR4A 3QQCE 1R0HA 4K9FA 4BY1L 1PFYA 3WWNB 3PL5A 2PYAA 2BE5D 3LNLA 2A6HD 5K2ME 2APOB 1K83L 5C4XL 3H0GL 1Y1WL 4AYBP 1DVBA 5IY0A 1B2OA 3K7AL 3S15L 4BXXL 4AHWA 1T9OA 2A69D 4A3FL 3JR7A 5MFZA 2CR8A 2YU9L 2B63L 3KYWA 3HJWB 3VPBE 2JI3A 3H9BA 2V0EA 4UY81 4QIWP 4ZN1B 3HOWL 2WAQP 3MSUA 3J7Y1 2HR5A 1WJVA 2PVXA 3GTML 4V196 3HOUL 3LWVB 3NFPI 1LTLA 5MLC3 2RFKB 2E2JL 3P2AA 5M3ML 2DSXA 1FHMA 1T9QA 5JVG1 4E6YA 5GAHc 3PKJA 3GTJL 1R0JA 3PZAA 1LKOA 3S1QL 4AR5A 2GMGA 5GAGc 3PO3L 1IU5A 2AYJA 2Y0SP 3CQZL 4XXBB 3PWFA 1YK5A 1IW7D 4JAFA
chains in the Genus database with same CATH topology
2M6OA 3K35A 4WFN1 1S30A 5DM71 4AI2A 2KKDA 4POGA 1BE7A 4TVMA 1VZGA 2H12A 2M6PA 4TPUA 1T9PA 1VCXA 3A44A 4JAEA 4ME3A 2JI2A 8RXNA 2V3BB 1B2JA 4RXNA 3ZG6A 1OWCA 1OWBA 1NXGA 5EINC 4JADA 2NYDA 4LHNA 5GADc 1CADA 2MS3A 1BRFA 2CKCA 2PVEA 2VL6A 1JYBA 2M4VA 4AHXA 1YUZA 5EIOC 5MGNA 3QVDA 4AR4A 1SMWA 1H7VA 3B08B 5H1Sc 2XJUA 3QQCE 1R0HA 3PIO1 4K9FA 1RWDA 1BQ9A 1FHHA 2LCQA 2A68D 2XJQA 3WWNB 3RYGA 1DX8A 2PYAA 4AR3A 2BE5D 3KYVA 3LNLA 3KYXA 4POFA 6RXNA 5AN9H 3KYUA 1C09A 2A6HD 2C6AA 1QCVA 2ZIXA 4AHZA 5K2ME 5GAEc 1SMMA 7RXNA 1B13A 4AHYA 3RZ6A 1R0IA 3P8BA 1QYBA 1DVBA 1NXEA 2XJPA 4YWMA 1B2OA 5IY0A 1RYTA 1ODHA 4AHWA 1T9OA 1YUXA 1S24A 2A6ED 4AI0A 2A69D 3LPEB 2KN9A 1R0FA 1CAAA 5MFZA 1IRNA 2CR8A 2XJSA 2XJTA 1S2ZA 5JVH1 2XJRA 3PIP1 2PSMC 3KYWA 3VPBE 1ZRPA 2JI3A 2V0EA 4UY81 4ZN1B 1VZHA 2PPTA 3IU3I 5MF6A 3RZTA 3MSUA 3MPSA 1LKPA 2J9UB 3J7Y1 1E8JA 2HR5A 1Z92B 4ZN3B 1WJVA 1NNQA 2PVXA 2XJVA 2M4YA 4V196 2V0FA 4B8CD 3NFPI 1LTLA 1YK4A 5MLC3 1RDVA 2L0ZA 2RDVA 1BFYA 3J7Z1 3KYYA 3P2AA 4YWLA 5DM61 2CKAA 5MFPA 4U671 3WWLA 1RYQA 4JAGA 2ERJA 4AR6A 5RXNA 4G6BA 1BQ8A 1RB9A 1FHMA 1T9QA 2DSXA 2K2DA 2ERSA 5JVG1 4AI3A 1IROA 4E6YA 5AI3A 5GAHc 3PKJA 2B5ID 1R0JA 3PZAA 1LKOA 1RDGA 1YV1A 4AR5A 4XGHA 1LKMA 4AI1A 3B0AB 2GMGA 5GAGc 1VZIA 1IU5A 2AYJA 3PKIA 2QL0A 4LHLA 4XXBB 2O5JD 2Z3RB 5AI2A 3SS2A 1SMUA 2JI1A 2Z3QB 3PWFA 4GS7D 1R0GA 1YK5A 1B71A 1IW7D 4JAFA 2C6BA 1IU6A
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 5GAE c;  4WFN 1;  5DM7 1;  3PIO 1;  4UY8 1;  5GAG c;  5GAH c;  5GAD c;  3J7Z 1;  5JVH 1;  4V19 6;  3PIP 1;  5DM6 1;  3J7Y 1;  4U67 1;  5H1S c;  5JVG 1;  5MLC 3; 
#chains in the Genus database with same CATH topology
 4WFN 1;  1SFO L;  1S30 A;  4POG A;  4BBS L;  3I4N L;  4TPU A;  2JA6 L;  1VCX A;  1OWB A;  1TWC L;  4JAD A;  1P7P A;  1CAD A;  3LWO B;  2E2H L;  1I3Q L;  4A3K L;  2CKC A;  2VL6 A;  5EIO C;  4A93 L;  1H7V A;  5H1S c;  1FHH A;  1DX8 A;  2PMZ P;  3KYV A;  4POF A;  2C6A A;  4A3D L;  4X6A L;  2JA5 L;  1B13 A;  3RZ6 A;  1R0I A;  2HVY C;  1QYB A;  1NXE A;  1TWG L;  1YUX A;  2VUM L;  3HKZ P;  1IRN A;  5FJ8 L;  2NVY L;  5JVH 1;  1ZRP A;  2PPT A;  3MPS A;  2J9U B;  5M3F L;  3GTP L;  1NNQ A;  2EY4 E;  3KYY A;  2CKA A;  4A3J L;  5MFP A;  4U67 1;  1RYQ A;  2ERJ A;  3MQK B;  1F4L A;  5M5X L;  2ERS A;  3GTL L;  1RDG A;  1YV1 A;  3HAX C;  1LKM A;  3B0A B;  3HOV L;  5C44 L;  3LWR B;  3S1M L;  3H3V M;  2QL0 A;  2NVX L;  2AUS B;  2Z3R B;  3SS2 A;  5M5W L;  2C6B A;  2M6O A;  4AI2 A;  3S16 L;  3GTK L;  1BE7 A;  3S17 L;  2M6P A;  2R92 L;  3FDJ A;  3A44 A;  8RXN A;  4A3L L;  1B2J A;  1NXG A;  3H99 A;  3S14 L;  4BBR L;  3PO2 L;  2PVE A;  1JYB A;  5MGN A;  4A3E L;  5M5Y L;  4C3J L;  3QVD A;  3B08 B;  5IYB L;  2XJU A;  1BQ9 A;  2LCQ A;  2A68 D;  3RYG A;  4AR3 A;  3KYX A;  4BY7 L;  6RXN A;  1QQT A;  3KYU A;  2AQC A;  2ZIX A;  3GTO L;  5GAE c;  3P8B A;  2XJP A;  4YWM A;  1RYT A;  1S24 A;  2A6E D;  3LPE B;  2KN9 A;  1R0F A;  1TWF L;  1CAA A;  2XJR A;  1PFV A;  2PSM C;  4A3I L;  3IU3 I;  5MF6 A;  3RZT A;  1PFW A;  1LKP A;  4ZN3 B;  2M4Y A;  4B8C D;  3HOY L;  3S1N L;  3M3Y L;  2WB1 P;  2L0Z A;  4A3G L;  3J7Z 1;  5DM6 1;  3HOZ L;  4JAG A;  3HOX L;  3RZD L;  2NVT L;  4AR6 A;  5RXN A;  4G6B A;  3LWQ B;  1RB9 A;  2K2D A;  2NVQ L;  4AI3 A;  1IRO A;  5AI3 A;  3S1R L;  5IYC L;  2B5I D;  3LWP B;  3PKI A;  5AI2 A;  1SMU A;  1PFU A;  2Z3Q B;  3I4M L;  2R7Z L;  1I50 L;  1I6H L;  3K35 A;  5DM7 1;  2H12 A;  1T9P A;  4C3H L;  1Y1V L;  4JAE A;  4ME3 A;  2JI2 A;  2V3B B;  4RXN A;  3H97 A;  5EIN C;  2NYD A;  4LHN A;  5C4J L;  2R93 L;  2M4V A;  1YUZ A;  1SMW A;  2E2I L;  3PIO 1;  1WCM L;  1RWD A;  2XJQ A;  5AN9 H;  1C09 A;  1QCV A;  4AHZ A;  5IP9 L;  2JA8 L;  1SMM A;  7RXN A;  4AHY A;  4A3C L;  1ODH A;  4Y52 L;  4A3B L;  3FKI L;  4AI0 A;  1R9T L;  2XJS A;  2XJT A;  1S2Z A;  3PIP 1;  3HJY B;  1VZH A;  4A3M L;  1E8J A;  1Z92 B;  4C2M 1;  5C3E L;  5IYD L;  2XJV A;  2V0F A;  1YK4 A;  1RDV A;  5FLM L;  2RDV A;  1BFY A;  4YWL A;  4C3I L;  3WWL A;  3H9C A;  3M4O L;  1BQ8 A;  1TWA L;  4XGH A;  4AI1 A;  3S2D L;  1VZI A;  5IP7 L;  4LHL A;  2O5J D;  1PZX A;  3S2H L;  2JI1 A;  1TWH L;  4GS7 D;  1R0G A;  1B71 A;  1IU6 A;  2KKD A;  4TVM A;  2JA7 L;  1VZG A;  3GTG L;  3RZO L;  4Y7N L;  3ZG6 A;  1OWC A;  5GAD c;  2MS3 A;  1BRF A;  4AHX A;  3GTQ L;  4AR4 A;  3QQC E;  1R0H A;  4K9F A;  4BY1 L;  1PFY A;  3WWN B;  3PL5 A;  2PYA A;  2BE5 D;  3LNL A;  2A6H D;  5K2M E;  2APO B;  1K83 L;  5C4X L;  3H0G L;  1Y1W L;  4AYB P;  1DVB A;  5IY0 A;  1B2O A;  3K7A L;  3S15 L;  4BXX L;  4AHW A;  1T9O A;  2A69 D;  4A3F L;  3JR7 A;  5MFZ A;  2CR8 A;  2YU9 L;  2B63 L;  3KYW A;  3HJW B;  3VPB E;  2JI3 A;  3H9B A;  2V0E A;  4UY8 1;  4QIW P;  4ZN1 B;  3HOW L;  2WAQ P;  3MSU A;  3J7Y 1;  2HR5 A;  1WJV A;  2PVX A;  3GTM L;  4V19 6;  3HOU L;  3LWV B;  3NFP I;  1LTL A;  5MLC 3;  2RFK B;  2E2J L;  3P2A A;  5M3M L;  2DSX A;  1FHM A;  1T9Q A;  5JVG 1;  4E6Y A;  5GAH c;  3PKJ A;  3GTJ L;  1R0J A;  3PZA A;  1LKO A;  3S1Q L;  4AR5 A;  2GMG A;  5GAG c;  3PO3 L;  1IU5 A;  2AYJ A;  2Y0S P;  3CQZ L;  4XXB B;  3PWF A;  1YK5 A;  1IW7 D;  4JAF A; 
#chains in the Genus database with same CATH homology
 2M6O A;  3K35 A;  4WFN 1;  1S30 A;  5DM7 1;  4AI2 A;  2KKD A;  4POG A;  1BE7 A;  4TVM A;  1VZG A;  2H12 A;  2M6P A;  4TPU A;  1T9P A;  1VCX A;  3A44 A;  4JAE A;  4ME3 A;  2JI2 A;  8RXN A;  2V3B B;  1B2J A;  4RXN A;  3ZG6 A;  1OWC A;  1OWB A;  1NXG A;  5EIN C;  4JAD A;  2NYD A;  4LHN A;  5GAD c;  1CAD A;  2MS3 A;  1BRF A;  2CKC A;  2PVE A;  2VL6 A;  1JYB A;  2M4V A;  4AHX A;  1YUZ A;  5EIO C;  5MGN A;  3QVD A;  4AR4 A;  1SMW A;  1H7V A;  3B08 B;  5H1S c;  2XJU A;  3QQC E;  1R0H A;  3PIO 1;  4K9F A;  1RWD A;  1BQ9 A;  1FHH A;  2LCQ A;  2A68 D;  2XJQ A;  3WWN B;  3RYG A;  1DX8 A;  2PYA A;  4AR3 A;  2BE5 D;  3KYV A;  3LNL A;  3KYX A;  4POF A;  6RXN A;  5AN9 H;  3KYU A;  1C09 A;  2A6H D;  2C6A A;  1QCV A;  2ZIX A;  4AHZ A;  5K2M E;  5GAE c;  1SMM A;  7RXN A;  1B13 A;  4AHY A;  3RZ6 A;  1R0I A;  3P8B A;  1QYB A;  1DVB A;  1NXE A;  2XJP A;  4YWM A;  1B2O A;  5IY0 A;  1RYT A;  1ODH A;  4AHW A;  1T9O A;  1YUX A;  1S24 A;  2A6E D;  4AI0 A;  2A69 D;  3LPE B;  2KN9 A;  1R0F A;  1CAA A;  5MFZ A;  1IRN A;  2CR8 A;  2XJS A;  2XJT A;  1S2Z A;  5JVH 1;  2XJR A;  3PIP 1;  2PSM C;  3KYW A;  3VPB E;  1ZRP A;  2JI3 A;  2V0E A;  4UY8 1;  4ZN1 B;  1VZH A;  2PPT A;  3IU3 I;  5MF6 A;  3RZT A;  3MSU A;  3MPS A;  1LKP A;  2J9U B;  3J7Y 1;  1E8J A;  2HR5 A;  1Z92 B;  4ZN3 B;  1WJV A;  1NNQ A;  2PVX A;  2XJV A;  2M4Y A;  4V19 6;  2V0F A;  4B8C D;  3NFP I;  1LTL A;  1YK4 A;  5MLC 3;  1RDV A;  2L0Z A;  2RDV A;  1BFY A;  3J7Z 1;  3KYY A;  3P2A A;  4YWL A;  5DM6 1;  2CKA A;  5MFP A;  4U67 1;  3WWL A;  1RYQ A;  4JAG A;  2ERJ A;  4AR6 A;  5RXN A;  4G6B A;  1BQ8 A;  1RB9 A;  1FHM A;  1T9Q A;  2DSX A;  2K2D A;  2ERS A;  5JVG 1;  4AI3 A;  1IRO A;  4E6Y A;  5AI3 A;  5GAH c;  3PKJ A;  2B5I D;  1R0J A;  3PZA A;  1LKO A;  1RDG A;  1YV1 A;  4AR5 A;  4XGH A;  1LKM A;  4AI1 A;  3B0A B;  2GMG A;  5GAG c;  1VZI A;  1IU5 A;  2AYJ A;  3PKI A;  2QL0 A;  4LHL A;  4XXB B;  2O5J D;  2Z3R B;  5AI2 A;  3SS2 A;  1SMU A;  2JI1 A;  2Z3Q B;  3PWF A;  4GS7 D;  1R0G A;  1YK5 A;  1B71 A;  1IW7 D;  4JAF A;  2C6B A;  1IU6 A; 
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similar chains in the Genus database (?% sequence similarity)
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similar chains in the pdb database (?% sequence similarity)

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