3PIO | Genus

Total Genus 17

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	17
sequence length	136
structure length	136
Chain Sequence	KRTKFRKQFRGRMTGDAKGGDYVAFGDYGLIAMEPAWIKSNQIEACRIVMSRHFRRGGKIYIRIFPDKPVTKKPAETRMGKGKGAVEYWVSVVKPGRVMFEVAGVTEEQAKEAFRLAGHKLPIQTKMVKREVYDEA

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

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The Resolver thinks Pdb

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Time for openFile(/file/5d17e43fc5216b383e4f5811/pdb.gz): 1130 ms

reading 136 atoms

ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false

1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.

Default Van der Waals type for model set to Jmol

136 atoms created

ModelSet: autobonding; use autobond=false to not generate bonds automatically

Time for creating model: 19 ms

Adding embedded #jmolscript: select ({0:135});backbone only;select *;

After clicking on a point (x,y) in the genus matrix above, a subchain from x to y is shown in color.

Genus data interpretation

Chord Diagram

molecule tags	Ribosome/antibiotic
publication title	Crystal structure of the synergistic antibiotic pair, lankamycin and lankacidin, in complex with the large ribosomal subunit. pubmed doi rcsb
molecule keywords	RIBOSOMAL 23S RNA
total genus	17
structure length	136
sequence length	136
ec nomenclature
pdb deposition date	2010-11-07

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
J	PF00252	Ribosomal_L16	Ribosomal protein L16p/L10e

Image from the rcsb pdb (www.rcsb.org)

cath code	Class	Architecture	Topology	Homology	Domain
3.90.1170.10	Alpha Beta	Alpha-Beta Complex	Aldehyde Oxidoreductase; domain 3	Ribosomal protein L10e/L16	3pioJ01

3CC2H 1M90J 1VQ5H 1VQLH 1VQ6H 3CPWH 5JVGJ 4UY8M 1YI2H 1K9MJ 5HL7J 3CC4H 3CCSH 1VQNH 3G6EH 3CF5J 5GAEN 1Y69K 1S72H 4WFBJ 3CCEH 4IOCJ 3G71H 3PIOJ 1YJ9H 3CCQH 3CCJH 1VQPH 3I55H 3CMAH 5GAGN 3PIPJ 5DM6J 3G4SH 5AN9F 1VQOH 2QA4H 2QEXH 1KC8J 1QVFH 3CXCH 3CC7H 2ZJRJ 1YJWH 1Q81J 2OTJH 1VQKH 3DLLJ 5GADN 3CD6H 5GAHN 1YITH 3I56H 1M1KJ 3CCRH 1VQ7H 1Q7YJ 4IOAJ 4WF9J 1K73J 2OTLH 1WKIA 3J7ZM 1N8RJ 1YIJH 4WCEJ 1VQ9H 1Q86J 3CCMH 2ZJQJ 1VQ8H 4IO9J 1NJIJ 1VQMH 1QVGH 1KQSH 1YJNH 1VQ4H 5H1SO 3CMEH 1YHQH 4U67J 1KD1J 4WFNJ 5MLCO 1Q82J 2ZJPJ 3CCUH 5DM7J 2PA2A 5JVHJ 3OW2H 4WFAJ 3CCVH 1W2BH 1K8AJ 1JJ2H 3CCLH
chains in the Genus database with same CATH superfamily

2Q5WE 3CC2H 4GA5A 1QPOA 1M90J 4GA4A 1VQ5H 5HUPA 4US8A 1VQLH 1VQ6H 1QPQA 1FFUB 3CPWH 3NRZC 5JVGJ 4UY8M 2QIEA 3NVYC 1YI2H 2WK6A 4YYYA 1K9MJ 3WO1A 4C7YA 2I14A 5HL7J 3CC4H 1FIQC 3CCSH 1VQNH 3G6EH 1WYGA 3CF5J 3C2OA 3EUB4 3C2RA 5HUOA 3RPFA 5GAEN 1Y69K 1S72H 1QAPA 4WFBJ 3CCEH 5AYZA 4IOCJ 3NS1C 3G71H 4LHMA 3PIOJ 3CCQH 1YJ9H 3CCJH 1JRPB 1VQPH 3AM9A 1N5WB 3I55H 3CMAH 5GAGN 1N62B 3PIPJ 1FM0E 5EY3A 5DM6J 4EAFA 1NVJA 3G4SH 5AN9F 3GNNA 4XR5A 2QEXH 2QA4H 1VQOH 1DGJA 1KC8J 1QVFH 5MPOC 1QPNA 2J0FA 1UOUA 3CXCH 4ZOHA 3CC7H 2B7NA 2ZJRJ 1YJWH 1Q81J 2OTJH 3NVZC 1VQKH 2WP4A 4EADA 3DLLJ 1OTPA 5GADN 1ZXIB 1O4UA 2E3TA 3CD6H 3TQVA 5GAHN 4KWWA 3FAHA 1YITH 4C7ZA 1BRWA 3AMZA 2I1OA 3I56H 1M1KJ 3NVWC 3CCRH 2W3RB 1VQ7H 3FC4A 1Q7YJ 4IOAJ 3BIIE 3WNZA 4WF9J 1K73J 5EP8A 2OTLH 1WKIA 3J7ZM 1N60B 1YTKA 1N8RJ 1RM6A 1AZYA 4YEKA 1N5XA 4C80A 2W55B 1YIJH 2W3SB 1N61B 4US9A 1FO4A 4WCEJ 3ETRC 1VQ9H 1Q86J 3CCMH 2ZJQJ 4USAA 3H5QA 4GA6A 1JROB 4AP8A 1VQ8H 2OMDA 5AYYA 3VMMA 4IO9J 1NJIJ 1VQMH 3L4PA 5HULA 1QVGH 2B7QA 1KQSH 1YJNH 1QPRA 3C2FA 1VQ4H 2TPTA 1SB3A 5H1SO 2DSJA 3CMEH 1YHQH 1SIJA 3L0GA 4U67J 3C2EA 1KD1J 3AN1A 5MLCO 4WFNJ 1YTDA 3PAJA 1Q82J 1NVIE 2W54B 2ZJPJ 4I9AA 3CCUH 5DM7J 2WK5A 3C2VA 2PA2A 5JVHJ 1FMAE 1X1OA 1V97A 3NVVC 5AYXA 3OW2H 3WO0A 3B9JC 1FFVB 1N63B 4WFAJ 4X46A 3CCVH 1VLBA 1W2BH 3SR6C 2B7PA 2JBMA 1K8AJ 1JJ2H 1VDVA 1YTEA 4KWVA 3CCLH
chains in the Genus database with same CATH topology

#chains in the Genus database with same CATH superfamily
 3CC2 H;  1M90 J;  1VQ5 H;  1VQL H;  1VQ6 H;  3CPW H;  5JVG J;  4UY8 M;  1YI2 H;  1K9M J;  5HL7 J;  3CC4 H;  3CCS H;  1VQN H;  3G6E H;  3CF5 J;  5GAE N;  1Y69 K;  1S72 H;  4WFB J;  3CCE H;  4IOC J;  3G71 H;  3PIO J;  1YJ9 H;  3CCQ H;  3CCJ H;  1VQP H;  3I55 H;  3CMA H;  5GAG N;  3PIP J;  5DM6 J;  3G4S H;  5AN9 F;  1VQO H;  2QA4 H;  2QEX H;  1KC8 J;  1QVF H;  3CXC H;  3CC7 H;  2ZJR J;  1YJW H;  1Q81 J;  2OTJ H;  1VQK H;  3DLL J;  5GAD N;  3CD6 H;  5GAH N;  1YIT H;  3I56 H;  1M1K J;  3CCR H;  1VQ7 H;  1Q7Y J;  4IOA J;  4WF9 J;  1K73 J;  2OTL H;  1WKI A;  3J7Z M;  1N8R J;  1YIJ H;  4WCE J;  1VQ9 H;  1Q86 J;  3CCM H;  2ZJQ J;  1VQ8 H;  4IO9 J;  1NJI J;  1VQM H;  1QVG H;  1KQS H;  1YJN H;  1VQ4 H;  5H1S O;  3CME H;  1YHQ H;  4U67 J;  1KD1 J;  4WFN J;  5MLC O;  1Q82 J;  2ZJP J;  3CCU H;  5DM7 J;  2PA2 A;  5JVH J;  3OW2 H;  4WFA J;  3CCV H;  1W2B H;  1K8A J;  1JJ2 H;  3CCL H; 
#chains in the Genus database with same CATH topology
 2Q5W E;  3CC2 H;  4GA5 A;  1QPO A;  1M90 J;  4GA4 A;  1VQ5 H;  5HUP A;  4US8 A;  1VQL H;  1VQ6 H;  1QPQ A;  1FFU B;  3CPW H;  3NRZ C;  5JVG J;  4UY8 M;  2QIE A;  3NVY C;  1YI2 H;  2WK6 A;  4YYY A;  1K9M J;  3WO1 A;  4C7Y A;  2I14 A;  5HL7 J;  3CC4 H;  1FIQ C;  3CCS H;  1VQN H;  3G6E H;  1WYG A;  3CF5 J;  3C2O A;  3EUB 4;  3C2R A;  5HUO A;  3RPF A;  5GAE N;  1Y69 K;  1S72 H;  1QAP A;  4WFB J;  3CCE H;  5AYZ A;  4IOC J;  3NS1 C;  3G71 H;  4LHM A;  3PIO J;  3CCQ H;  1YJ9 H;  3CCJ H;  1JRP B;  1VQP H;  3AM9 A;  1N5W B;  3I55 H;  3CMA H;  5GAG N;  1N62 B;  3PIP J;  1FM0 E;  5EY3 A;  5DM6 J;  4EAF A;  1NVJ A;  3G4S H;  5AN9 F;  3GNN A;  4XR5 A;  2QEX H;  2QA4 H;  1VQO H;  1DGJ A;  1KC8 J;  1QVF H;  5MPO C;  1QPN A;  2J0F A;  1UOU A;  3CXC H;  4ZOH A;  3CC7 H;  2B7N A;  2ZJR J;  1YJW H;  1Q81 J;  2OTJ H;  3NVZ C;  1VQK H;  2WP4 A;  4EAD A;  3DLL J;  1OTP A;  5GAD N;  1ZXI B;  1O4U A;  2E3T A;  3CD6 H;  3TQV A;  5GAH N;  4KWW A;  3FAH A;  1YIT H;  4C7Z A;  1BRW A;  3AMZ A;  2I1O A;  3I56 H;  1M1K J;  3NVW C;  3CCR H;  2W3R B;  1VQ7 H;  3FC4 A;  1Q7Y J;  4IOA J;  3BII E;  3WNZ A;  4WF9 J;  1K73 J;  5EP8 A;  2OTL H;  1WKI A;  3J7Z M;  1N60 B;  1YTK A;  1N8R J;  1RM6 A;  1AZY A;  4YEK A;  1N5X A;  4C80 A;  2W55 B;  1YIJ H;  2W3S B;  1N61 B;  4US9 A;  1FO4 A;  4WCE J;  3ETR C;  1VQ9 H;  1Q86 J;  3CCM H;  2ZJQ J;  4USA A;  3H5Q A;  4GA6 A;  1JRO B;  4AP8 A;  1VQ8 H;  2OMD A;  5AYY A;  3VMM A;  4IO9 J;  1NJI J;  1VQM H;  3L4P A;  5HUL A;  1QVG H;  2B7Q A;  1KQS H;  1YJN H;  1QPR A;  3C2F A;  1VQ4 H;  2TPT A;  1SB3 A;  5H1S O;  2DSJ A;  3CME H;  1YHQ H;  1SIJ A;  3L0G A;  4U67 J;  3C2E A;  1KD1 J;  3AN1 A;  5MLC O;  4WFN J;  1YTD A;  3PAJ A;  1Q82 J;  1NVI E;  2W54 B;  2ZJP J;  4I9A A;  3CCU H;  5DM7 J;  2WK5 A;  3C2V A;  2PA2 A;  5JVH J;  1FMA E;  1X1O A;  1V97 A;  3NVV C;  5AYX A;  3OW2 H;  3WO0 A;  3B9J C;  1FFV B;  1N63 B;  4WFA J;  4X46 A;  3CCV H;  1VLB A;  1W2B H;  3SR6 C;  2B7P A;  2JBM A;  1K8A J;  1JJ2 H;  1VDV A;  1YTE A;  4KWV A;  3CCL H; 
#chains in the Genus database with same CATH homology
 3CC2 H;  1M90 J;  1VQ5 H;  1VQL H;  1VQ6 H;  3CPW H;  5JVG J;  4UY8 M;  1YI2 H;  1K9M J;  5HL7 J;  3CC4 H;  3CCS H;  1VQN H;  3G6E H;  3CF5 J;  5GAE N;  1Y69 K;  1S72 H;  4WFB J;  3CCE H;  4IOC J;  3G71 H;  3PIO J;  1YJ9 H;  3CCQ H;  3CCJ H;  1VQP H;  3I55 H;  3CMA H;  5GAG N;  3PIP J;  5DM6 J;  3G4S H;  5AN9 F;  1VQO H;  2QA4 H;  2QEX H;  1KC8 J;  1QVF H;  3CXC H;  3CC7 H;  2ZJR J;  1YJW H;  1Q81 J;  2OTJ H;  1VQK H;  3DLL J;  5GAD N;  3CD6 H;  5GAH N;  1YIT H;  3I56 H;  1M1K J;  3CCR H;  1VQ7 H;  1Q7Y J;  4IOA J;  4WF9 J;  1K73 J;  2OTL H;  1WKI A;  3J7Z M;  1N8R J;  1YIJ H;  4WCE J;  1VQ9 H;  1Q86 J;  3CCM H;  2ZJQ J;  1VQ8 H;  4IO9 J;  1NJI J;  1VQM H;  1QVG H;  1KQS H;  1YJN H;  1VQ4 H;  5H1S O;  3CME H;  1YHQ H;  4U67 J;  1KD1 J;  4WFN J;  5MLC O;  1Q82 J;  2ZJP J;  3CCU H;  5DM7 J;  2PA2 A;  5JVH J;  3OW2 H;  4WFA J;  3CCV H;  1W2B H;  1K8A J;  1JJ2 H;  3CCL H;

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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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3PIOJ

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations