5DM71

Crystal structure of the 50s ribosomal subunit from deinococcus radiodurans in complex with hygromycin a
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
54
structure length
54
Chain Sequence
b'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 3
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 5dm7100
5GAHc 5DM71 3J7Y1 5MLC3 4V196 5GAGc 4WFN1 5DM61 3PIO1 4UY81 5H1Sc 3PIP1 5JVG1 4U671 5GADc 5JVH1 3J7Z1 5GAEc
chains in the Genus database with same CATH superfamily
5M5XL 3S1QL 3HOWL 3I4ML 1R0HA 1R0FA 1R0IA 3WWLA 2ERJA 3GTOL 1VZGA 5RXNA 3H99A 2XJTA 2MS3A 1BQ8A 5JVH1 2KN9A 1NXGA 5IP7L 2A68D 2C6BA 1CAAA 5IYBL 1S24A 1OWBA 2NVTL 1K83L 1TWFL 3P8BA 1S30A 4A3FL 5GAHc 4A3BL 2DSXA 3GTJL 1PFWA 1RYTA 4C3HL 1YUXA 2XJPA 4A3LL 4A3DL 3RZDL 2M4YA 3M4OL 2VUML 2O5JD 1I50L 2V0FA 3LWVB 5MF6A 4XXBB 4C3JL 3VPBE 3J7Z1 3K35A 1WCML 1VZIA 3PIO1 4AR3A 2H12A 4C3IL 2AQCA 3GTML 3KYWA 4AI0A 4JADA 4AHYA 3S1ML 3PKJA 3PL5A 3S1NL 3H3VM 5IYDL 4UY81 4K9FA 3H97A 2A6ED 1R0GA 2KKDA 5AN9H 4AHXA 3MQKB 1VCXA 2GMGA 6RXNA 1RB9A 4E6YA 3HOVL 1SMMA 5GAGc 2C6AA 2XJVA 3HJYB 1I6HL 4G6BA 2JI2A 3H9CA 3QQCE 1P7PA 2AYJA 3PO2L 1OWCA 1BFYA 1B2OA 4ZN3B 3CQZL 1DX8A 5FLML 1FHMA 2LCQA 2ERSA 4JAFA 2AUSB 4BY7L 3M3YL 2A69D 1VZHA 4A3ML 2NYDA 8RXNA 2JI1A 2Y0SP 3P2AA 3MPSA 3RZOL 1B71A 4A3GL 5C4JL 1I3QL 3HJWB 3B0AB 2RDVA 1IRNA 4AI3A 2QL0A 3S2HL 3KYUA 2E2IL 1SMWA 3J7Y1 4AI2A 1CADA 2Z3QB 1C09A 2VL6A 2NVQL 4JAGA 1QCVA 5C44L 4AYBP 5AI2A 4A3IL 3NFPI 2XJQA 2E2JL 1T9PA 3HOZL 3HOUL 4AR5A 3K7AL 4A3EL 4AR4A 1S2ZA 2XJRA 2V3BB 2V0EA 2HVYC 2M4VA 3S1RL 4WFN1 4C2M1 1T9QA 3HKZP 4BBRL 3S2DL 1YUZA 4GS7D 1B13A 1IROA 2CR8A 3B08B 1LKOA 4LHNA 2L0ZA 1Y1VL 5EIOC 4U671 1T9OA 4Y52L 1RDGA 1PFUA 4A3CL 1E8JA 1F4LA 2CKCA 3HAXC 3S15L 3KYXA 4TPUA 1NXEA 2PPTA 2WAQP 1QQTA 3PZAA 4BY1L 1BQ9A 1PFVA 5MLC3 2JA6L 2HR5A 2E2HL 2M6PA 1ZRPA 3KYVA 3PKIA 5MFPA 1QYBA 3GTKL 5JVG1 5MFZA 5C3EL 2JA8L 3H0GL 3SS2A 1BRFA 4X6AL 5M3FL 1TWAL 1YK5A 4BBSL 5IY0A 3ZG6A 3LNLA 1PFYA 4A3KL 4ZN1B 5GAEc 1LKPA 3HOYL 2Z3RB 3PIP1 4JAEA 3GTGL 4QIWP 4A3JL 5FJ8L 4YWLA 2NVXL 1TWGL 2XJUA 2R93L 2JA5L 3HOXL 1R0JA 2EY4E 1Y1WL 3A44A 5MGNA 3S16L 5IP9L 4LHLA 2B5ID 5M5YL 1LTLA 2CKAA 2M6OA 3GTPL 4B8CD 1SMUA 3LWRB 3S14L 2K2DA 1FHHA 5H1Sc 3WWNB 1B2JA 2JI3A 1SFOL 3IU3I 5M5WL 3QVDA 3KYYA 4AHZA 3I4NL 4BXXL 5K2ME 1IU5A 1NNQA 4A93L 5M3ML 2PVXA 5EINC 5GADc 2WB1P 4ME3A 2ZIXA 5DM71 3LWPB 1LKMA 2PMZP 4YWMA 4TVMA 3H9BA 2APOB 1H7VA 2YU9L 3PWFA 4XGHA 1IU6A 2J9UB 3FDJA 1RYQA 4Y7NL 3S17L 1JYBA 1RDVA 3LWOB 1WJVA 5DM61 3JR7A 4AR6A 3GTLL 5IYCL 3PO3L 2XJSA 2R7ZL 1R9TL 4V196 4AI1A 2RFKB 2JA7L 2A6HD 3RZ6A 2PYAA 2PSMC 3MSUA 2NVYL 7RXNA 1ODHA 2PVEA 5C4XL 2R92L 3RZTA 1IW7D 4POGA 1TWCL 1BE7A 1TWHL 4RXNA 3LPEB 2BE5D 4AHWA 3LWQB 1YK4A 3GTQL 1PZXA 5AI3A 3RYGA 4POFA 1Z92B 1RWDA 1DVBA 3FKIL 2B63L 1YV1A
chains in the Genus database with same CATH topology
3IU3I 1SMMA 5GAGc 2CR8A 2C6AA 3QVDA 3KYYA 4AHZA 2XJVA 1LKOA 3B08B 1R0HA 1R0FA 5K2ME 1IU5A 1NNQA 1R0IA 4LHNA 4G6BA 2JI2A 3WWLA 2L0ZA 2PVXA 2ERJA 5EINC 5EIOC 4U671 1T9OA 5GADc 4ME3A 2ZIXA 5DM71 3QQCE 1VZGA 1RDGA 5RXNA 1LKMA 2AYJA 4YWMA 1OWCA 1BFYA 1E8JA 4TVMA 2CKCA 1B2OA 2XJTA 4ZN3B 2MS3A 1H7VA 1BQ8A 3KYXA 4TPUA 1NXEA 2PPTA 3PWFA 5JVH1 1DX8A 4XGHA 1IU6A 2J9UB 2KN9A 1NXGA 1RYQA 2A68D 1FHMA 2C6BA 3PZAA 1BQ9A 1JYBA 2LCQA 5MLC3 2HR5A 2ERSA 4JAFA 2M6PA 1CAAA 1S24A 2A69D 1RDVA 1OWBA 1VZHA 1ZRPA 2NYDA 3KYVA 3PKIA 5MFPA 1QYBA 1WJVA 5DM61 8RXNA 2JI1A 3P8BA 5JVG1 1S30A 5MFZA 3P2AA 4AR6A 3MPSA 1B71A 5GAHc 3SS2A 2DSXA 1BRFA 2RDVA 2XJSA 3B0AB 1IRNA 4AI3A 1YK5A 1RYTA 5IY0A 1YUXA 2QL0A 1IROA 4V196 4AI1A 2XJPA 2A6HD 3KYUA 3RZ6A 1SMWA 2M4YA 2PYAA 3ZG6A 2PSMC 3MSUA 2O5JD 3LNLA 3J7Y1 4AI2A 1CADA 2V0FA 2Z3QB 1C09A 2VL6A 7RXNA 4ZN1B 1ODHA 5GAEc 2PVEA 1LKPA 4JAGA 2Z3RB 5MF6A 1QCVA 4XXBB 3PIP1 4JAEA 3RZTA 3VPBE 5AI2A 3NFPI 1IW7D 4POGA 2XJQA 4YWLA 1T9PA 1BE7A 2XJUA 4RXNA 3J7Z1 3K35A 1R0JA 4AR5A 1VZIA 3A44A 2JI3A 3PIO1 4AR3A 5MGNA 4AR4A 3LPEB 2H12A 1S2ZA 2XJRA 4LHLA 2B5ID 2BE5D 3KYWA 1LTLA 4AHWA 2CKAA 2V3BB 2V0EA 2M6OA 4AI0A 1YK4A 4JADA 2M4VA 4AHYA 4B8CD 1SMUA 4WFN1 3PKJA 5AI3A 3RYGA 1T9QA 4POFA 1FHHA 4UY81 4K9FA 2A6ED 1R0GA 2KKDA 5AN9H 1Z92B 1RWDA 1DVBA 1YUZA 4AHXA 4GS7D 5H1Sc 1B13A 1VCXA 2GMGA 1RB9A 4E6YA 6RXNA 2K2DA 3WWNB 1B2JA 1YV1A
chains in the Genus database with same CATH homology


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