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


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