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
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
publication title Cryo-EM structure of the spinach chloroplast ribosome reveals the location of plastid-specific ribosomal proteins and extensions.
pubmed doi rcsb
molecule tags Ribosome
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
5MLC9 1DD5A 3LHPS 4L8IA 4KB4A 1EH1A 4OYDB 4KC6A 1WQGA 4JLRC 4KB2A 3LF9A 5JSNB 1WQHA 5JSBB 1GE9A 1EK8A 1WQFA 4GFQA 4KAWX 4KDDA 1IS1A 1Y698 1ISEA
chains in the Genus database with same CATH superfamily
1TL8A 3K57A 1V9MA 1Y1WA 3LHPS 1YNJD 1NH3A 1IW7D 2E2IA 1RR8C 2VUMA 1EH1A 3K5MA 3K58A 2E2HA 4OYDB 3GTJA 2A68D 5JSNB 1ZYRD 4IP8A 2R92A 1I50A 1WQHA 2A6ED 5CQGA 3DU5A 3DU6A 4Q5GA 4C2MA 3M4AA 1GE9A 1EK8A 2WB1A 2B63A 3SJRA 1SEUA 1K4SA 2F4QA 1WCMA 2BE5D 1R49A 4FYDA 2JA7A 2R93A 1A36A 4IP9A 1TWCA 1R5ZA 1SMYD 1WQGA 3H0GA 1T8IA 1I3QA 2B9SB 1MIUA 1HQMD 5JSBB 3IAYA 2A69D 1I6VD 4D3ZA 1LPQA 1Y1VA 1WQFA 3MAQA 4NOLA 2A6HD 2NVXA 4AHCA 1Y698 5C9HA 1SFOA 2R4GA 3KYLA 2JA5A 4L8IA 4NOKA 4AN8A 4NOMA 4AYBA 1R9TA 3K59A 3GTLA 3GTPA 4H3TA 1SC7A 1TWAA 1TGOA 4KC6A 2NVYA 4JLRC 4KB2A 4QCLA 3GTGA 4FXDA 1ISEA 2CW0D 3K5NA 1TWGA 1YNND 1Q8IA 1DD5A 4D3YA 4EJ3A 4F3EA 5MLC9 4Q5VA 4FGUA 4LMOA 2R7ZA 3WVOA 4KB4A 1TWHA 2WAQA 2JA6A 3HKZA 3P9AA 1TWFA 3GTQA 3K5OA 4O26A 3LF9A 3GTMA 1A35A 2Y0SA 3GTOA 1A31A 2O5JD 1K83A 3CQZA 4QIWA 3GTKA 3FKIA 4GFQA 1RRJA 4KAWX 2YU9A 2PMZA 4KDDA 3K5LA 1IS1A 1EJ9A 1K4TA
chains in the Genus database with same CATH topology
1TL8A 3K57A 1V9MA 1Y1WA 3LHPS 1YNJD 1NH3A 1IW7D 2E2IA 1RR8C 2VUMA 1EH1A 3K5MA 3K58A 2E2HA 4OYDB 3GTJA 2A68D 5JSNB 1ZYRD 4IP8A 2R92A 1I50A 1WQHA 2A6ED 5CQGA 3DU5A 3DU6A 4Q5GA 4C2MA 3M4AA 1GE9A 1EK8A 2WB1A 2B63A 3SJRA 1SEUA 1K4SA 2F4QA 1WCMA 2BE5D 1R49A 4FYDA 2JA7A 2R93A 1A36A 4IP9A 1TWCA 1R5ZA 1SMYD 1WQGA 3H0GA 1T8IA 1I3QA 2B9SB 1MIUA 1HQMD 5JSBB 3IAYA 2A69D 1I6VD 4D3ZA 1LPQA 1Y1VA 1WQFA 3MAQA 4NOLA 2A6HD 2NVXA 4AHCA 1Y698 5C9HA 1SFOA 2R4GA 3KYLA 2JA5A 4L8IA 4NOKA 4AN8A 4NOMA 4AYBA 1R9TA 3K59A 3GTLA 3GTPA 4H3TA 1SC7A 1TWAA 1TGOA 4KC6A 2NVYA 4JLRC 4KB2A 4QCLA 3GTGA 4FXDA 1ISEA 2CW0D 3K5NA 1TWGA 1YNND 1Q8IA 1DD5A 4D3YA 4EJ3A 4F3EA 5MLC9 4Q5VA 4FGUA 4LMOA 2R7ZA 3WVOA 4KB4A 1TWHA 2WAQA 2JA6A 3HKZA 3P9AA 1TWFA 3GTQA 3K5OA 4O26A 3LF9A 3GTMA 1A35A 2Y0SA 3GTOA 1A31A 2O5JD 1K83A 3CQZA 4QIWA 3GTKA 3FKIA 4GFQA 1RRJA 4KAWX 2YU9A 2PMZA 4KDDA 3K5LA 1IS1A 1EJ9A 1K4TA
chains in the Genus database with same CATH homology


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