5MLC9

Cryo-em structure of the spinach chloroplast ribosome reveals the location of plastid-specific ribosomal proteins and extensions
Total Genus 34
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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
34
sequence length
183
structure length
107
Chain Sequence
b'SLIETNTKQRMEKTIETIRSNFNSVRLTSDRRKELAKVVSKLAEEGKVAVRNIRRDALKSYEKLEKEKKLSEDNVKDLSADLQKLTDEYMKKVESIYKQKEQELMKV'
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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 23S ribosomal RNA, chloroplastic
molecule tags Ribosome
publication title Cryo-EM structure of the spinach chloroplast ribosome reveals the location of plastid-specific ribosomal proteins and extensions.
pubmed doi rcsb
total genus 34
structure length 107
sequence length 183
ec nomenclature
pdb deposition date 2016-12-06

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
9 PF01765 RRF Ribosome recycling factor
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
1.10.132.20 Mainly Alpha Orthogonal Bundle Topoisomerase I; Chain A, domain 4 Topoisomerase I; Chain A, domain 4 5mlc900
4JLRC 4KC6A 1Y698 4KAWX 1DD5A 4KDDA 1GE9A 1ISEA 5JSNB 5JSBB 1WQGA 3LHPS 4KB2A 1EK8A 1WQHA 4GFQA 5MLC9 1WQFA 1EH1A 4KB4A 4OYDB 1IS1A 4L8IA 3LF9A
chains in the Genus database with same CATH superfamily
1A31A 3MAQA 2A6HD 3HKZA 3DU6A 1LPQA 4F3EA 1K83A 1R9TA 1DD5A 2JA7A 1GE9A 1YNND 2E2IA 3DU5A 1T8IA 2PMZA 4AN8A 1TL8A 3LHPS 3SJRA 3K57A 2R4GA 3K5LA 2B63A 1SEUA 3GTLA 4D3ZA 4LMOA 1WCMA 2E2HA 4KB4A 3K5MA 4L8IA 4Q5VA 1R49A 3H0GA 4EJ3A 2R7ZA 1K4TA 1A35A 1Y698 2A68D 4KAWX 4FGUA 3GTGA 3GTKA 2JA6A 5JSNB 2Y0SA 1SFOA 3K5NA 1EK8A 3GTOA 1RRJA 4NOKA 2A69D 2NVXA 4GFQA 2O5JD 1Y1VA 4AHCA 1WQFA 1RR8C 3P9AA 4OYDB 1IS1A 1I3QA 2A6ED 3K58A 2WAQA 3K59A 3GTMA 1EJ9A 4NOLA 1TWGA 1TWCA 4KC6A 3WVOA 3GTPA 1HQMD 4KDDA 4FYDA 1ISEA 5JSBB 2BE5D 2NVYA 4IP9A 5CQGA 2R93A 3M4AA 4AYBA 4NOMA 5C9HA 4QCLA 1SMYD 1TWAA 3K5OA 5MLC9 1Y1WA 2WB1A 2F4QA 4H3TA 1V9MA 2YU9A 2JA5A 1Q8IA 1ZYRD 3IAYA 2R92A 1TWFA 1TWHA 4FXDA 1IW7D 3CQZA 4JLRC 4QIWA 1SC7A 4Q5GA 1WQGA 3GTJA 1I50A 4KB2A 3GTQA 1K4SA 4O26A 1YNJD 1WQHA 3KYLA 4C2MA 1MIUA 2B9SB 3FKIA 1R5ZA 1I6VD 1TGOA 1NH3A 4D3YA 1A36A 2VUMA 1EH1A 2CW0D 4IP8A 3LF9A
chains in the Genus database with same CATH topology
1A31A 3MAQA 2A6HD 3HKZA 3DU6A 1LPQA 4F3EA 1K83A 1R9TA 1DD5A 2JA7A 1GE9A 1YNND 2E2IA 3DU5A 1T8IA 2PMZA 4AN8A 1TL8A 3LHPS 3SJRA 3K57A 2R4GA 3K5LA 2B63A 1SEUA 3GTLA 4D3ZA 4LMOA 1WCMA 2E2HA 4KB4A 3K5MA 4L8IA 4Q5VA 1R49A 3H0GA 4EJ3A 2R7ZA 1K4TA 1A35A 1Y698 2A68D 4KAWX 4FGUA 3GTGA 3GTKA 2JA6A 5JSNB 2Y0SA 1SFOA 3K5NA 1EK8A 3GTOA 1RRJA 4NOKA 2A69D 2NVXA 4GFQA 2O5JD 1Y1VA 4AHCA 1WQFA 1RR8C 3P9AA 4OYDB 1IS1A 1I3QA 2A6ED 3K58A 2WAQA 3K59A 3GTMA 1EJ9A 4NOLA 1TWGA 1TWCA 4KC6A 3WVOA 3GTPA 1HQMD 4KDDA 4FYDA 1ISEA 5JSBB 2BE5D 2NVYA 4IP9A 5CQGA 2R93A 3M4AA 4AYBA 4NOMA 5C9HA 4QCLA 1SMYD 1TWAA 3K5OA 5MLC9 1Y1WA 2WB1A 2F4QA 4H3TA 1V9MA 2YU9A 2JA5A 1Q8IA 1ZYRD 3IAYA 2R92A 1TWFA 1TWHA 4FXDA 1IW7D 3CQZA 4JLRC 4QIWA 1SC7A 4Q5GA 1WQGA 3GTJA 1I50A 4KB2A 3GTQA 1K4SA 4O26A 1YNJD 1WQHA 3KYLA 4C2MA 1MIUA 2B9SB 3FKIA 1R5ZA 1I6VD 1TGOA 1NH3A 4D3YA 1A36A 2VUMA 1EH1A 2CW0D 4IP8A 3LF9A
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 4JLR C;  4KC6 A;  1Y69 8;  4KAW X;  1DD5 A;  4KDD A;  1GE9 A;  1ISE A;  5JSN B;  5JSB B;  1WQG A;  3LHP S;  4KB2 A;  1EK8 A;  1WQH A;  4GFQ A;  5MLC 9;  1WQF A;  1EH1 A;  4KB4 A;  4OYD B;  1IS1 A;  4L8I A;  3LF9 A; 
#chains in the Genus database with same CATH topology
 1A31 A;  3MAQ A;  2A6H D;  3HKZ A;  3DU6 A;  1LPQ A;  4F3E A;  1K83 A;  1R9T A;  1DD5 A;  2JA7 A;  1GE9 A;  1YNN D;  2E2I A;  3DU5 A;  1T8I A;  2PMZ A;  4AN8 A;  1TL8 A;  3LHP S;  3SJR A;  3K57 A;  2R4G A;  3K5L A;  2B63 A;  1SEU A;  3GTL A;  4D3Z A;  4LMO A;  1WCM A;  2E2H A;  4KB4 A;  3K5M A;  4L8I A;  4Q5V A;  1R49 A;  3H0G A;  4EJ3 A;  2R7Z A;  1K4T A;  1A35 A;  1Y69 8;  2A68 D;  4KAW X;  4FGU A;  3GTG A;  3GTK A;  2JA6 A;  5JSN B;  2Y0S A;  1SFO A;  3K5N A;  1EK8 A;  3GTO A;  1RRJ A;  4NOK A;  2A69 D;  2NVX A;  4GFQ A;  2O5J D;  1Y1V A;  4AHC A;  1WQF A;  1RR8 C;  3P9A A;  4OYD B;  1IS1 A;  1I3Q A;  2A6E D;  3K58 A;  2WAQ A;  3K59 A;  3GTM A;  1EJ9 A;  4NOL A;  1TWG A;  1TWC A;  4KC6 A;  3WVO A;  3GTP A;  1HQM D;  4KDD A;  4FYD A;  1ISE A;  5JSB B;  2BE5 D;  2NVY A;  4IP9 A;  5CQG A;  2R93 A;  3M4A A;  4AYB A;  4NOM A;  5C9H A;  4QCL A;  1SMY D;  1TWA A;  3K5O A;  5MLC 9;  1Y1W A;  2WB1 A;  2F4Q A;  4H3T A;  1V9M A;  2YU9 A;  2JA5 A;  1Q8I A;  1ZYR D;  3IAY A;  2R92 A;  1TWF A;  1TWH A;  4FXD A;  1IW7 D;  3CQZ A;  4JLR C;  4QIW A;  1SC7 A;  4Q5G A;  1WQG A;  3GTJ A;  1I50 A;  4KB2 A;  3GTQ A;  1K4S A;  4O26 A;  1YNJ D;  1WQH A;  3KYL A;  4C2M A;  1MIU A;  2B9S B;  3FKI A;  1R5Z A;  1I6V D;  1TGO A;  1NH3 A;  4D3Y A;  1A36 A;  2VUM A;  1EH1 A;  2CW0 D;  4IP8 A;  3LF9 A; 
#chains in the Genus database with same CATH homology
 1A31 A;  3MAQ A;  2A6H D;  3HKZ A;  3DU6 A;  1LPQ A;  4F3E A;  1K83 A;  1R9T A;  1DD5 A;  2JA7 A;  1GE9 A;  1YNN D;  2E2I A;  3DU5 A;  1T8I A;  2PMZ A;  4AN8 A;  1TL8 A;  3LHP S;  3SJR A;  3K57 A;  2R4G A;  3K5L A;  2B63 A;  1SEU A;  3GTL A;  4D3Z A;  4LMO A;  1WCM A;  2E2H A;  4KB4 A;  3K5M A;  4L8I A;  4Q5V A;  1R49 A;  3H0G A;  4EJ3 A;  2R7Z A;  1K4T A;  1A35 A;  1Y69 8;  2A68 D;  4KAW X;  4FGU A;  3GTG A;  3GTK A;  2JA6 A;  5JSN B;  2Y0S A;  1SFO A;  3K5N A;  1EK8 A;  3GTO A;  1RRJ A;  4NOK A;  2A69 D;  2NVX A;  4GFQ A;  2O5J D;  1Y1V A;  4AHC A;  1WQF A;  1RR8 C;  3P9A A;  4OYD B;  1IS1 A;  1I3Q A;  2A6E D;  3K58 A;  2WAQ A;  3K59 A;  3GTM A;  1EJ9 A;  4NOL A;  1TWG A;  1TWC A;  4KC6 A;  3WVO A;  3GTP A;  1HQM D;  4KDD A;  4FYD A;  1ISE A;  5JSB B;  2BE5 D;  2NVY A;  4IP9 A;  5CQG A;  2R93 A;  3M4A A;  4AYB A;  4NOM A;  5C9H A;  4QCL A;  1SMY D;  1TWA A;  3K5O A;  5MLC 9;  1Y1W A;  2WB1 A;  2F4Q A;  4H3T A;  1V9M A;  2YU9 A;  2JA5 A;  1Q8I A;  1ZYR D;  3IAY A;  2R92 A;  1TWF A;  1TWH A;  4FXD A;  1IW7 D;  3CQZ A;  4JLR C;  4QIW A;  1SC7 A;  4Q5G A;  1WQG A;  3GTJ A;  1I50 A;  4KB2 A;  3GTQ A;  1K4S A;  4O26 A;  1YNJ D;  1WQH A;  3KYL A;  4C2M A;  1MIU A;  2B9S B;  3FKI A;  1R5Z A;  1I6V D;  1TGO A;  1NH3 A;  4D3Y A;  1A36 A;  2VUM A;  1EH1 A;  2CW0 D;  4IP8 A;  3LF9 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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