5DM61

Crystal structure of the 50s ribosomal subunit from deinococcus radiodurans
Total Genus 5
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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
5
sequence length
54
structure length
54
Chain Sequence
AAAGAAPRIIVKMESSAGTGFYYTTTKNRRNTQAKLELKKYDPVAAHVVFAAAA
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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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publication title Crystallographic characterization of the ribosomal binding site and molecular mechanism of action of Hygromycin A.
pubmed doi rcsb
molecule tags Ribosome
molecule keywords 50S ribosomal protein L1
total genus 5
structure length 54
sequence length 54
ec nomenclature
pdb deposition date 2015-09-08
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 5dm6100
4V196 5H1Sc 5MLC3 5GAEc 5GAHc 5DM71 5JVG1 5GADc 5DM61 5JVH1 5GAGc 4U671 3J7Z1 4WFN1 3J7Y1 3PIO1 4UY81 3PIP1
chains in the Genus database with same CATH superfamily
2GMGA 1RDGA 5IY0A 1H7VA 5GADc 3M3YL 2MS3A 1WCML 2C6AA 3KYWA 3GTKL 3M4OL 6RXNA 4AR5A 4ZN3B 5C4JL 4BXXL 1QQTA 1IU6A 1E8JA 4QIWP 2CR8A 4BY1L 4JAGA 3PIO1 5JVG1 2JA5L 2CKCA 5GAEc 5M5XL 3MSUA 2NVTL 3S1QL 3FDJA 3RYGA 1YV1A 5EINC 3KYVA 1YK5A 1OWBA 4YWMA 1SMMA 4A3BL 1SFOL 1VZGA 1T9OA 5M5WL 3HOXL 3RZOL 3PIP1 3H9CA 1DX8A 3J7Y1 3WWLA 3KYYA 2KKDA 3A44A 1ZRPA 2VUML 1LKOA 1RWDA 1PFYA 4A3KL 4LHLA 5IP7L 3S15L 3LWRB 1YUXA 8RXNA 2A6HD 3HOZL 2WB1P 3H99A 3KYUA 2J9UB 1I6HL 1K83L 4A3FL 4A3CL 2Y0SP 1VCXA 3HJYB 2JI1A 4WFN1 2B5ID 2E2HL 4U671 5M3FL 4AR3A 3S1NL 1T9QA 3K7AL 4Y7NL 2RDVA 2NVXL 5GAHc 1I3QL 2RFKB 1TWGL 4C3HL 3PKIA 2R92L 4A3LL 1B2JA 3GTJL 5FJ8L 1NXGA 3LWOB 2PPTA 2NVYL 4A3ML 2C6BA 1R0FA 2PYAA 1IW7D 2NVQL 5AI2A 5MFZA 2XJVA 3GTGL 3HOVL 2XJRA 4GS7D 1QCVA 1IU5A 1CAAA 3PL5A 4AHXA 5RXNA 2JI3A 2NYDA 3QVDA 4YWLA 3K35A 3GTLL 1CADA 4A3DL 2QL0A 2K2DA 2PVXA 4TPUA 2V0EA 1R0JA 1VZIA 2JA6L 4JADA 2M4YA 2XJTA 3VPBE 1T9PA 3H3VM 3GTQL 3MQKB 3H97A 5C44L 4XXBB 1LKPA 1DVBA 5FLML 2VL6A 3IU3I 3RZ6A 4K9FA 3GTPL 1B2OA 3KYXA 3HJWB 2E2IL 2ERJA 5H1Sc 2M6PA 4C3IL 2PMZP 2CKAA 1IROA 4C3JL 1IRNA 4POFA 4BBSL 3S16L 1YK4A 4A93L 4BY7L 5MFPA 1TWHL 2DSXA 5DM61 3HOWL 1NNQA 1RYTA 3PKJA 4AYBP 4X6AL 4RXNA 4A3EL 2ZIXA 1S30A 1Z92B 5C3EL 2YU9L 3HOUL 1PZXA 3LWVB 4AR6A 3HKZP 1NXEA 3FKIL 1SMWA 1S24A 2Z3RB 3ZG6A 1P7PA 2R7ZL 1BQ9A 2PVEA 5M5YL 3S1RL 3LPEB 5EIOC 2KN9A 2ERSA 3JR7A 3I4NL 1C09A 1TWAL 2XJQA 3GTML 5JVH1 2H12A 1B71A 3NFPI 2XJSA 4AI1A 1FHHA 5MGNA 3HOYL 2EY4E 4Y52L 5C4XL 3WWNB 4AR4A 1F4LA 4B8CD 4V196 2PSMC 3S1ML 2V0FA 3H9BA 1QYBA 3RZDL 3MPSA 2JA7L 1VZHA 4A3IL 2XJPA 3S2DL 2A68D 3RZTA 3P8BA 1RYQA 1TWCL 5AN9H 1BQ8A 2BE5D 2M6OA 4AI0A 3PO3L 4AI3A 2WAQP 4POGA 1RB9A 1YUZA 2M4VA 4LHNA 1LTLA 2HR5A 5M3ML 2O5JD 5MF6A 1OWCA 2L0ZA 3LNLA 5GAGc 4JAFA 1Y1VL 2XJUA 2AUSB 1R0GA 3LWQB 1B13A 1WJVA 2A6ED 1ODHA 5IYCL 3SS2A 3S2HL 1BFYA 1TWFL 4ZN1B 3P2AA 1FHMA 1RDVA 2Z3QB 2B63L 5MLC3 5IYBL 1PFVA 5IP9L 1PFUA 4AHWA 3LWPB 3PO2L 4UY81 1I50L 3B0AB 2JA8L 2A69D 3H0GL 1Y1WL 3GTOL 1BRFA 3PZAA 2E2JL 4A3GL 4BBRL 1PFWA 4G6BA 3PWFA 1LKMA 3CQZL 3QQCE 1R0IA 3B08B 5DM71 4A3JL 3J7Z1 2APOB 2R93L 2HVYC 4AHZA 4XGHA 1R9TL 1SMUA 2JI2A 4AI2A 7RXNA 4ME3A 4JAEA 3S17L 1S2ZA 4TVMA 1JYBA 1BE7A 2V3BB 3HAXC 5K2ME 4E6YA 2AYJA 5IYDL 5AI3A 2LCQA 4C2M1 3S14L 3I4ML 1R0HA 2AQCA 4AHYA
chains in the Genus database with same CATH topology
2GMGA 4RXNA 1NXGA 1RDGA 5IY0A 1H7VA 1OWCA 5GADc 2L0ZA 2ZIXA 1S30A 2PPTA 1Z92B 3LNLA 4AR6A 2MS3A 2C6AA 5GAGc 2C6BA 3KYWA 4JAFA 1NXEA 1R0FA 2PYAA 6RXNA 2XJUA 1IW7D 4AR5A 4ZN3B 1R0GA 1B13A 1WJVA 5AI2A 1SMWA 1IU6A 1S24A 2A6ED 2Z3RB 3ZG6A 5MFZA 1ODHA 1E8JA 2XJVA 3SS2A 2XJRA 2CR8A 1BQ9A 1BFYA 4GS7D 1QCVA 4ZN1B 2PVEA 4JAGA 3P2AA 3PIO1 1FHMA 5JVG1 1RDVA 2Z3QB 1IU5A 5MLC3 2CKCA 1CAAA 3LPEB 5EIOC 2KN9A 2ERSA 5GAEc 3MSUA 1C09A 4AHXA 5RXNA 2JI3A 2NYDA 3RYGA 1YV1A 3QVDA 5EINC 3KYVA 1YK5A 1OWBA 2XJQA 4YWLA 3K35A 4AHWA 1CADA 5JVH1 4UY81 4YWMA 2QL0A 1SMMA 2K2DA 2PVXA 2H12A 3B0AB 4TPUA 1B71A 1VZGA 3NFPI 2A69D 1T9OA 2XJSA 2V0EA 4AI1A 3PIP1 1FHHA 5MGNA 1BRFA 3PZAA 1R0JA 1DX8A 1VZIA 3J7Y1 3WWLA 4G6BA 4JADA 2M4YA 3PWFA 3KYYA 1LKMA 2KKDA 2XJTA 3A44A 3QQCE 1R0IA 1ZRPA 3B08B 3WWNB 4AR4A 4B8CD 3VPBE 5DM71 3J7Z1 1LKOA 4V196 2PSMC 1RWDA 1T9PA 4LHLA 2V0FA 4AHZA 4XGHA 1QYBA 3MPSA 1YUXA 8RXNA 2A6HD 1SMUA 1NNQA 4XXBB 1VZHA 1LKPA 2JI2A 1DVBA 4AI2A 2VL6A 3IU3I 2XJPA 3RZ6A 4K9FA 3KYUA 7RXNA 1B2OA 2A68D 4JAEA 3KYXA 2J9UB 4ME3A 3RZTA 1VCXA 3P8BA 2JI1A 4WFN1 1RYQA 2B5ID 2ERJA 1BQ8A 2BE5D 5H1Sc 5AN9H 2M6OA 2M6PA 4AI0A 4U671 4AI3A 1S2ZA 2CKAA 4TVMA 1IROA 1JYBA 4AR3A 1IRNA 1BE7A 4POGA 2V3BB 4POFA 1RB9A 1YK4A 1T9QA 1YUZA 2M4VA 5K2ME 4E6YA 2AYJA 4LHNA 2RDVA 5GAHc 1LTLA 5AI3A 2HR5A 2LCQA 5MFPA 2O5JD 3PKIA 2DSXA 1R0HA 4AHYA 5DM61 5MF6A 1B2JA 1RYTA 3PKJA
chains in the Genus database with same CATH homology


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