4U67 | Genus

Total Genus 21

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	21
sequence length	175
structure length	175
Chain Sequence	MELTAKPRTPKQKLDESMIAAVAYNKENNVSFALDRKAFDRAFRQQSTTGLFDITVEGGETFPALVKAVQMDKRKRAPIHVDFYMVTYGEPVEVSVPVHTTGRSQGEVQGGLVDIVVHNLQIVAPGPRRIPQELVVDVTKMNIGDHITAGDIKLPEGCTLAADPELTVVSVLPPR

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/5d17465a55b2170ef5ef2f41/pdb.gz): 1292 ms

reading 175 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

175 atoms created

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

Time for creating model: 22 ms

Adding embedded #jmolscript: select ({0:174});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
publication title	The Ribosomal Protein uL22 Modulates the Shape of the Protein Exit Tunnel. pubmed doi rcsb
molecule keywords	50S ribosomal protein L2
total genus	21
structure length	175
sequence length	175
ec nomenclature
pdb deposition date	2014-07-28

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
S	PF01386	Ribosomal_L25p	Ribosomal L25p family
S	PF14693	Ribosomal_TL5_C	Ribosomal protein TL5, C-terminal domain

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

cath code	Class	Architecture	Topology	Homology	Domain
2.40.240.10	Mainly Beta	Beta Barrel	Ribosomal Protein L25; Chain P	Ribosomal Protein L25; Chain P	4u67S01
2.170.120.20	Mainly Beta	Beta Complex	RNA Polymerase Alpha Subunit; Chain A, domain 2	Ribosomal protein L25, beta domain	4u67S02

5JVGS 2HZ7A 4IO9S 4IOCS 4WFAS 1NYLA 2ZJQS 1FEUA 5DM7S 1QRUA 3PIOS 5IZNA 4UY88 5GADW 4WCES 4IOAS 1B75A 5HL7S 1QRTA 5GAEW 1O0BA 5DM6S 4P2BA 5GAGW 1D6KA 1QRSA 3J7ZV 3CF5S 4JYZA 5BNZA 1QTQA 1EXDA 4WFNS 1EUQA 1EUYA 1ZJWA 2ZJRS 2RD2A 3AIIA 1GTSA 1GTRA 4H3SA 3PIPS 4JXXA 1O0CA 4JXZA 2RE8A 1DFUP 5JVHS 3DLLS 4WF9S 2ZJPS 5GAHW 4WFBS 4U67S
chains in the Genus database with same CATH superfamily

3HOXC 2KQ1A 2WB1D 2HZ7A 3PO2C 4H4KA 4WFAS 3W2WB 4A3BC 2ZJQS 4BY7C 1BDFA 5C4XC 2Z0YA 3RZOC 1FEUA 4G7ZA 4A3KC 2KPUA 1QRUA 1TWAC 2YU9C 4A3EC 4XLNA 3PO3C 2NVYC 2R92C 2PNWA 5IZNA 2G5DA 4WCES 3GTKC 1B75A 1YNNA 5IYBC 1SMYA 4E8BA 1VHYA 3HOUC 4JK1A 4KN7A 4YFXA 2JA8C 3CF5S 2B63C 2GAEA 2EGVA 4BBRC 4XSZA 3S17C 1EUYA 1Y1VC 2O5JA 2PA8D 3M3YC 4JXXA 3EQLA 3S1MC 2ZJPS 2JA5C 4BXXC 2PJJA 4WFBS 1ZYRA 2NVTC 4A3CC 2G6GA 5JVGS 4GZYA 4IO9S 3S15C 3HOVC 2KXYA 4IOCS 3S2HC 3LYWA 3GTGC 1NXZA 1HQMA 1TWHC 3HKZD 3CZBA 4XSXA 4OIOA 3PIOS 4YFKA 3X1LB 2PMZD 1I6VA 2CX8A 5IYCC 4IOAS 5IP7C 2O5IA 1YNJA 3RZDC 3S2DC 4C2MC 5GAEW 1O0BA 2PICA 4Y52C 5DM6S 4YG2A 5HQHA 4A3DC 4AYBD 2NWAA 4JYZA 5BNZA 1EUQA 1K83C 1TWGC 2A69A 4A3MC 1I3QC 2E2IC 3AIIA 3HOZC 2Y0SD 3S1RC 1DFUP 5IYDC 1Y1WC 2JA7C 1Z85A 4LK0A 3DXJA 4X6AC 5D4DA 2A6EA 3HOYC 4C3HC 4A3FC 3GTLC 3GTQC 2E2HC 3WODA 3GTPC 4A3JC 2A6HA 2JA6C 2CW0A 5TMCA 4LJZA 3I4NC 1I6HC 1WCMC 3H0GC 4OIRA 2E2JC 4UY88 4QIWD 4Q5SA 5GADW 2NVQC 1IW7A 1TWCC 2R93C 3S1NC 4BY1C 2EGWA 5HL7S 3S14C 4OINA 4A3GC 4QJVA 4P2BA 5GAGW 3K7AC 3GTJC 4G7OA 4KMUA 2L3UA 4KN4A 1QTQA 5FLMC 3GTMC 1EXDA 3S1QC 4ZH4A 4OIQA 4J3CA 2VUMC 4BBSC 1ZJWA 3I4MC 2RD2A 4XLPA 2R7ZC 4L69A 4H3SA 5TMFA 2RE8A 4MEYA 3HOWC 1UDXA 3DLLS 3S16C 5GAHW 4NOIA 4A93C 4U67S 4OIPA 2NVXC 4MEXA 1NYLA 2AE0X 5IP9C 1TWFC 5DM7S 2A68A 2BE5A 3CQZC 1SFOC 1I50C 2PPBA 3GTOC 2WAQD 4Y7NC 1R9TC 4A3LC 1VHKA 2L5NA 4C3IC 4A3IC 1QRTA 4Q4ZA 3H3VD 3M4OC 1D6KA 1QRSA 4MQ9A 3J7ZV 5C44C 4G7HA 2PI8A 4WFNS 5C4JC 3FKIC 2ZJRS 1GTRA 1GTSA 3PIPS 4JXZA 1V6ZA 1O0CA 4LLGA 4YFNA 3W2VB 5JVHS 4LK1A 4WF9S 4C3JC 5C3EC 4V194 3KW2A
chains in the Genus database with same CATH topology

5JVGS 2HZ7A 4IO9S 4H4KA 4WFAS 1NYLA 3W2WB 2ZJQS 4IOCS 1FEUA 5DM7S 1QRUA 3PIOS 3X1LB 5IZNA 4UY88 5GADW 4WCES 4IOAS 1B75A 5HL7S 1QRTA 5GAEW 1O0BA 5DM6S 4P2BA 5GAGW 1D6KA 1QRSA 3J7ZV 3CF5S 4JYZA 5BNZA 1QTQA 1EXDA 4WFNS 1EUQA 1EUYA 1ZJWA 2ZJRS 2RD2A 3AIIA 1GTSA 1GTRA 4H3SA 3PIPS 4JXXA 1O0CA 4JXZA 2RE8A 3W2VB 5JVHS 1DFUP 1UDXA 3DLLS 2ZJPS 4WF9S 5GAHW 4WFBS 4U67S 4V194
chains in the Genus database with same CATH homology

#chains in the Genus database with same CATH superfamily
 5JVG S;  2HZ7 A;  4IO9 S;  4IOC S;  4WFA S;  1NYL A;  2ZJQ S;  1FEU A;  5DM7 S;  1QRU A;  3PIO S;  5IZN A;  4UY8 8;  5GAD W;  4WCE S;  4IOA S;  1B75 A;  5HL7 S;  1QRT A;  5GAE W;  1O0B A;  5DM6 S;  4P2B A;  5GAG W;  1D6K A;  1QRS A;  3J7Z V;  3CF5 S;  4JYZ A;  5BNZ A;  1QTQ A;  1EXD A;  4WFN S;  1EUQ A;  1EUY A;  1ZJW A;  2ZJR S;  2RD2 A;  3AII A;  1GTS A;  1GTR A;  4H3S A;  3PIP S;  4JXX A;  1O0C A;  4JXZ A;  2RE8 A;  1DFU P;  5JVH S;  3DLL S;  4WF9 S;  2ZJP S;  5GAH W;  4WFB S;  4U67 S; 
#chains in the Genus database with same CATH topology
 3HOX C;  2KQ1 A;  2WB1 D;  2HZ7 A;  3PO2 C;  4H4K A;  4WFA S;  3W2W B;  4A3B C;  2ZJQ S;  4BY7 C;  1BDF A;  5C4X C;  2Z0Y A;  3RZO C;  1FEU A;  4G7Z A;  4A3K C;  2KPU A;  1QRU A;  1TWA C;  2YU9 C;  4A3E C;  4XLN A;  3PO3 C;  2NVY C;  2R92 C;  2PNW A;  5IZN A;  2G5D A;  4WCE S;  3GTK C;  1B75 A;  1YNN A;  5IYB C;  1SMY A;  4E8B A;  1VHY A;  3HOU C;  4JK1 A;  4KN7 A;  4YFX A;  2JA8 C;  3CF5 S;  2B63 C;  2GAE A;  2EGV A;  4BBR C;  4XSZ A;  3S17 C;  1EUY A;  1Y1V C;  2O5J A;  2PA8 D;  3M3Y C;  4JXX A;  3EQL A;  3S1M C;  2ZJP S;  2JA5 C;  4BXX C;  2PJJ A;  4WFB S;  1ZYR A;  2NVT C;  4A3C C;  2G6G A;  5JVG S;  4GZY A;  4IO9 S;  3S15 C;  3HOV C;  2KXY A;  4IOC S;  3S2H C;  3LYW A;  3GTG C;  1NXZ A;  1HQM A;  1TWH C;  3HKZ D;  3CZB A;  4XSX A;  4OIO A;  3PIO S;  4YFK A;  3X1L B;  2PMZ D;  1I6V A;  2CX8 A;  5IYC C;  4IOA S;  5IP7 C;  2O5I A;  1YNJ A;  3RZD C;  3S2D C;  4C2M C;  5GAE W;  1O0B A;  2PIC A;  4Y52 C;  5DM6 S;  4YG2 A;  5HQH A;  4A3D C;  4AYB D;  2NWA A;  4JYZ A;  5BNZ A;  1EUQ A;  1K83 C;  1TWG C;  2A69 A;  4A3M C;  1I3Q C;  2E2I C;  3AII A;  3HOZ C;  2Y0S D;  3S1R C;  1DFU P;  5IYD C;  1Y1W C;  2JA7 C;  1Z85 A;  4LK0 A;  3DXJ A;  4X6A C;  5D4D A;  2A6E A;  3HOY C;  4C3H C;  4A3F C;  3GTL C;  3GTQ C;  2E2H C;  3WOD A;  3GTP C;  4A3J C;  2A6H A;  2JA6 C;  2CW0 A;  5TMC A;  4LJZ A;  3I4N C;  1I6H C;  1WCM C;  3H0G C;  4OIR A;  2E2J C;  4UY8 8;  4QIW D;  4Q5S A;  5GAD W;  2NVQ C;  1IW7 A;  1TWC C;  2R93 C;  3S1N C;  4BY1 C;  2EGW A;  5HL7 S;  3S14 C;  4OIN A;  4A3G C;  4QJV A;  4P2B A;  5GAG W;  3K7A C;  3GTJ C;  4G7O A;  4KMU A;  2L3U A;  4KN4 A;  1QTQ A;  5FLM C;  3GTM C;  1EXD A;  3S1Q C;  4ZH4 A;  4OIQ A;  4J3C A;  2VUM C;  4BBS C;  1ZJW A;  3I4M C;  2RD2 A;  4XLP A;  2R7Z C;  4L69 A;  4H3S A;  5TMF A;  2RE8 A;  4MEY A;  3HOW C;  1UDX A;  3DLL S;  3S16 C;  5GAH W;  4NOI A;  4A93 C;  4U67 S;  4OIP A;  2NVX C;  4MEX A;  1NYL A;  2AE0 X;  5IP9 C;  1TWF C;  5DM7 S;  2A68 A;  2BE5 A;  3CQZ C;  1SFO C;  1I50 C;  2PPB A;  3GTO C;  2WAQ D;  4Y7N C;  1R9T C;  4A3L C;  1VHK A;  2L5N A;  4C3I C;  4A3I C;  1QRT A;  4Q4Z A;  3H3V D;  3M4O C;  1D6K A;  1QRS A;  4MQ9 A;  3J7Z V;  5C44 C;  4G7H A;  2PI8 A;  4WFN S;  5C4J C;  3FKI C;  2ZJR S;  1GTR A;  1GTS A;  3PIP S;  4JXZ A;  1V6Z A;  1O0C A;  4LLG A;  4YFN A;  3W2V B;  5JVH S;  4LK1 A;  4WF9 S;  4C3J C;  5C3E C;  4V19 4;  3KW2 A; 
#chains in the Genus database with same CATH homology
 5JVG S;  2HZ7 A;  4IO9 S;  4H4K A;  4WFA S;  1NYL A;  3W2W B;  2ZJQ S;  4IOC S;  1FEU A;  5DM7 S;  1QRU A;  3PIO S;  3X1L B;  5IZN A;  4UY8 8;  5GAD W;  4WCE S;  4IOA S;  1B75 A;  5HL7 S;  1QRT A;  5GAE W;  1O0B A;  5DM6 S;  4P2B A;  5GAG W;  1D6K A;  1QRS A;  3J7Z V;  3CF5 S;  4JYZ A;  5BNZ A;  1QTQ A;  1EXD A;  4WFN S;  1EUQ A;  1EUY A;  1ZJW A;  2ZJR S;  2RD2 A;  3AII A;  1GTS A;  1GTR A;  4H3S A;  3PIP S;  4JXX A;  1O0C A;  4JXZ A;  2RE8 A;  3W2V B;  5JVH S;  1DFU P;  1UDX A;  3DLL S;  2ZJP S;  4WF9 S;  5GAH W;  4WFB S;  4U67 S;  4V19 4;

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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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4U67S

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations