5D1M | Genus

Total Genus 46

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	46
sequence length	146
structure length	146
Chain Sequence	ALKRIHKELNDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDYPFKPPKVAFTTRIYHPNINSNGSICLDILRSQWSPALTISKVLLSICSLLCDPNPDDPLVPEIARIYKTDREKYNRIAREWTQKYAM

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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Viewer cachePut cache://localLOAD_/file/5d00ebd441eb126e43d2b935/pdb.gz

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The Resolver thinks Pdb

loadScript /static/js/j2s/core/corebio.z.js

Time for openFile(/file/5d00ebd441eb126e43d2b935/pdb.gz): 1804 ms

reading 146 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

146 atoms created

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

Time for creating model: 19 ms

Adding embedded #jmolscript: select ({0:145});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	Ligase
source organism	Homo sapiens
publication title	Insights into Ubiquitination from the Unique Clamp-like Binding of the RING E3 AO7 to the E2 UbcH5B. pubmed doi rcsb
molecule keywords	Ubiquitin-conjugating enzyme E2 D2
total genus	46
structure length	146
sequence length	146
ec nomenclature	ec 2.3.2.23: E2 ubiquitin-conjugating enzyme.
pdb deposition date	2015-08-04

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF00179	UQ_con	Ubiquitin-conjugating enzyme

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

cath code	Class	Architecture	Topology	Homology	Domain
3.10.110.10	Alpha Beta	Roll	Ubiquitin Conjugating Enzyme	Ubiquitin Conjugating Enzyme	5d1mA00

4AP4B 2FUHA 4NRIA 2YB6A 3OBUA 2OXQA 2AAKA 2H2YA 2K07A 2KLYA 1FXTA 4LDTC 5D1MA 2KJHA 3PTFA 4BVUB 3O2UA 2C2VB 4ONLB 2O25A 1FZYA 3R3QA 2UCZA 2AYVA 2PX9B 3FSHA 2ONUA 3K9OA 5AITD 2C2VC 1M4QA 5EGGA 4NR3B 4NRGB 3KPAA 1X23A 1J7DB 3VONB 3CEGA 3OBSA 1Z3DA 1J7DA 4V3LA 5IFRA 2DAYA 4YIIU 1KPQA 2OB4A 2E2CA 1Z5SA 5D1KA 3FN1B 5FERB 2PWQA 2F4WA 5D0MA 1YH2A 3BZHA 4DHZF 3VONC 4QPLB 4Q5EC 2Z6OA 2AWFA 3OBXA 1S1QA 3F92A 1U9BA 2C4PA 2YBFA 4M1NA 4DHJC 3SQVC 1YLAA 1U9AA 2Z6PA 5AIEB 3UIPA 4II2C 2EBKA 1Y8XA 2EKEA 3H8KA 4S3OA 5D2MA 1PZVA 4ONLA 4DHID 3HCUB 4EJEA 3SY2C 2CLWB 1WZWA 4JUEA 2NVUC 5HPTC 5F6VA 4DS2A 4DDGA 1FBVC 1ZUOA 1J74A 1QCQA 1ZDNA 2ESKA 1Y6LA 1AYZA 3OJ4A 2EDIA 4NRGA 4NR3A 3RZ3A 1TTEA 2GMIB 3L1YA 5JNEB 1KPSA 2Z5DA 2GRQA 2YHOB 4FH1A 2LXPA 1Q34A 3ONGB 3ZQSA 1C4ZD 2F4ZA 4YC1A 3OBQA 1UKXA 4A49B 5F6WA 1M4PA 3ZNIC 2YZ0A 1A3SA 4IP3B 2EBMA 4CCGA 4V3KA 2DAXA 4W5VA 2F0RA 4ONMB 1JBBA 3A4SA 3UIOA 4Q5HC 5F6DA 3RCZB 2UYZA 4R62A 4WZ3A 4A4BC 1JASA 4ONNB 1YRVA 4P5OG 4TKPA 2BEPA 2CLWA 3WE5A 1JATB 2Y9PA 2QGXA 2FO3A 4ZNYA 5KNLC 2XWUA 2DAWA 5D1LA 3HCTB 3E95C 3JW0A 5AIUB 1KPPA 2CYXA 4NRIB 5F6UA 2R0JA 3UGBA 2PE6A 2Y4WA 1UZXA 2GMIA 4AUQA 2VRRA 3EVXA 1Z2UA 1WZVA 3R42A 4L83A 4Y1LC 3W31B 2GRRA 3JVZA 4MDKA 1ZGUA 2ESQA 2ESPA 5F6YA 4BWFA 3K9PA 2GROA 2Q0VA 2A4DA 5D0KA 5FQ2A 2Y9MA 5AITB 4DDIA 3TGDA 3P9HA 2HLWA 2GJDA 2A7LA 2ESOA 4ONMA 2DMFA 3P9GA 4X57A 2O25C 4JQUA 3UINA 4LADA 3E46A 3E95A 1YF9A 3A33A 5DFLA 1W4UA 2GRPA 4ONNA 2BF8A 4A4CC 1JATA 4GPRA 5F6XA 1I7KA 3RPGA 5F6EA 3EB6B 2MT6A 3L1ZA 4Y1LA 2GRNA
chains in the Genus database with same CATH superfamily

#chains in the Genus database with same CATH superfamily
 4AP4 B;  2FUH A;  4NRI A;  2YB6 A;  3OBU A;  2OXQ A;  2AAK A;  2H2Y A;  2K07 A;  2KLY A;  1FXT A;  4LDT C;  5D1M A;  2KJH A;  3PTF A;  4BVU B;  3O2U A;  2C2V B;  4ONL B;  2O25 A;  1FZY A;  3R3Q A;  2UCZ A;  2AYV A;  2PX9 B;  3FSH A;  2ONU A;  3K9O A;  5AIT D;  2C2V C;  1M4Q A;  5EGG A;  4NR3 B;  4NRG B;  3KPA A;  1X23 A;  1J7D B;  3VON B;  3CEG A;  3OBS A;  1Z3D A;  1J7D A;  4V3L A;  5IFR A;  2DAY A;  4YII U;  1KPQ A;  2OB4 A;  2E2C A;  1Z5S A;  5D1K A;  3FN1 B;  5FER B;  2PWQ A;  2F4W A;  5D0M A;  1YH2 A;  3BZH A;  4DHZ F;  3VON C;  4QPL B;  4Q5E C;  2Z6O A;  2AWF A;  3OBX A;  1S1Q A;  3F92 A;  1U9B A;  2C4P A;  2YBF A;  4M1N A;  4DHJ C;  3SQV C;  1YLA A;  1U9A A;  2Z6P A;  5AIE B;  3UIP A;  4II2 C;  2EBK A;  1Y8X A;  2EKE A;  3H8K A;  4S3O A;  5D2M A;  1PZV A;  4ONL A;  4DHI D;  3HCU B;  4EJE A;  3SY2 C;  2CLW B;  1WZW A;  4JUE A;  2NVU C;  5HPT C;  5F6V A;  4DS2 A;  4DDG A;  1FBV C;  1ZUO A;  1J74 A;  1QCQ A;  1ZDN A;  2ESK A;  1Y6L A;  1AYZ A;  3OJ4 A;  2EDI A;  4NRG A;  4NR3 A;  3RZ3 A;  1TTE A;  2GMI B;  3L1Y A;  5JNE B;  1KPS A;  2Z5D A;  2GRQ A;  2YHO B;  4FH1 A;  2LXP A;  1Q34 A;  3ONG B;  3ZQS A;  1C4Z D;  2F4Z A;  4YC1 A;  3OBQ A;  1UKX A;  4A49 B;  5F6W A;  1M4P A;  3ZNI C;  2YZ0 A;  1A3S A;  4IP3 B;  2EBM A;  4CCG A;  4V3K A;  2DAX A;  4W5V A;  2F0R A;  4ONM B;  1JBB A;  3A4S A;  3UIO A;  4Q5H C;  5F6D A;  3RCZ B;  2UYZ A;  4R62 A;  4WZ3 A;  4A4B C;  1JAS A;  4ONN B;  1YRV A;  4P5O G;  4TKP A;  2BEP A;  2CLW A;  3WE5 A;  1JAT B;  2Y9P A;  2QGX A;  2FO3 A;  4ZNY A;  5KNL C;  2XWU A;  2DAW A;  5D1L A;  3HCT B;  3E95 C;  3JW0 A;  5AIU B;  1KPP A;  2CYX A;  4NRI B;  5F6U A;  2R0J A;  3UGB A;  2PE6 A;  2Y4W A;  1UZX A;  2GMI A;  4AUQ A;  2VRR A;  3EVX A;  1Z2U A;  1WZV A;  3R42 A;  4L83 A;  4Y1L C;  3W31 B;  2GRR A;  3JVZ A;  4MDK A;  1ZGU A;  2ESQ A;  2ESP A;  5F6Y A;  4BWF A;  3K9P A;  2GRO A;  2Q0V A;  2A4D A;  5D0K A;  5FQ2 A;  2Y9M A;  5AIT B;  4DDI A;  3TGD A;  3P9H A;  2HLW A;  2GJD A;  2A7L A;  2ESO A;  4ONM A;  2DMF A;  3P9G A;  4X57 A;  2O25 C;  4JQU A;  3UIN A;  4LAD A;  3E46 A;  3E95 A;  1YF9 A;  3A33 A;  5DFL A;  1W4U A;  2GRP A;  4ONN A;  2BF8 A;  4A4C C;  1JAT A;  4GPR A;  5F6X A;  1I7K A;  3RPG A;  5F6E A;  3EB6 B;  2MT6 A;  3L1Z A;  4Y1L A;  2GRN A; 
#chains in the Genus database with same CATH topology
 4AP4 B;  2FUH A;  4NRI A;  2YB6 A;  3OBU A;  2OXQ A;  2AAK A;  2H2Y A;  2K07 A;  2KLY A;  1FXT A;  4LDT C;  5D1M A;  2KJH A;  3PTF A;  4BVU B;  3O2U A;  2C2V B;  4ONL B;  2O25 A;  1FZY A;  3R3Q A;  2UCZ A;  2AYV A;  2PX9 B;  3FSH A;  2ONU A;  3K9O A;  5AIT D;  2C2V C;  1M4Q A;  5EGG A;  4NR3 B;  4NRG B;  3KPA A;  1X23 A;  1J7D B;  3VON B;  3CEG A;  3OBS A;  1Z3D A;  1J7D A;  4V3L A;  5IFR A;  2DAY A;  4YII U;  1KPQ A;  2OB4 A;  2E2C A;  1Z5S A;  5D1K A;  3FN1 B;  5FER B;  2PWQ A;  2F4W A;  5D0M A;  1YH2 A;  3BZH A;  4DHZ F;  3VON C;  4QPL B;  4Q5E C;  2Z6O A;  2AWF A;  3OBX A;  1S1Q A;  3F92 A;  1U9B A;  2C4P A;  2YBF A;  4M1N A;  4DHJ C;  3SQV C;  1YLA A;  1U9A A;  2Z6P A;  5AIE B;  3UIP A;  4II2 C;  2EBK A;  1Y8X A;  2EKE A;  3H8K A;  4S3O A;  5D2M A;  1PZV A;  4ONL A;  4DHI D;  3HCU B;  4EJE A;  3SY2 C;  2CLW B;  1WZW A;  4JUE A;  2NVU C;  5HPT C;  5F6V A;  4DS2 A;  4DDG A;  1FBV C;  1ZUO A;  1J74 A;  1QCQ A;  1ZDN A;  2ESK A;  1Y6L A;  1AYZ A;  3OJ4 A;  2EDI A;  4NRG A;  4NR3 A;  3RZ3 A;  1TTE A;  2GMI B;  3L1Y A;  5JNE B;  1KPS A;  2Z5D A;  2GRQ A;  2YHO B;  4FH1 A;  2LXP A;  1Q34 A;  3ONG B;  3ZQS A;  1C4Z D;  2F4Z A;  4YC1 A;  3OBQ A;  1UKX A;  4A49 B;  5F6W A;  1M4P A;  3ZNI C;  2YZ0 A;  1A3S A;  4IP3 B;  2EBM A;  4CCG A;  4V3K A;  2DAX A;  4W5V A;  2F0R A;  4ONM B;  1JBB A;  3A4S A;  3UIO A;  4Q5H C;  5F6D A;  3RCZ B;  2UYZ A;  4R62 A;  4WZ3 A;  4A4B C;  1JAS A;  4ONN B;  1YRV A;  4P5O G;  4TKP A;  2BEP A;  2CLW A;  3WE5 A;  1JAT B;  2Y9P A;  2QGX A;  2FO3 A;  4ZNY A;  5KNL C;  2XWU A;  2DAW A;  5D1L A;  3HCT B;  3E95 C;  3JW0 A;  5AIU B;  1KPP A;  2CYX A;  4NRI B;  5F6U A;  2R0J A;  3UGB A;  2PE6 A;  2Y4W A;  1UZX A;  2GMI A;  4AUQ A;  2VRR A;  3EVX A;  1Z2U A;  1WZV A;  3R42 A;  4L83 A;  4Y1L C;  3W31 B;  2GRR A;  3JVZ A;  4MDK A;  1ZGU A;  2ESQ A;  2ESP A;  5F6Y A;  4BWF A;  3K9P A;  2GRO A;  2Q0V A;  2A4D A;  5D0K A;  5FQ2 A;  2Y9M A;  5AIT B;  4DDI A;  3TGD A;  3P9H A;  2HLW A;  2GJD A;  2A7L A;  2ESO A;  4ONM A;  2DMF A;  3P9G A;  4X57 A;  2O25 C;  4JQU A;  3UIN A;  4LAD A;  3E46 A;  3E95 A;  1YF9 A;  3A33 A;  5DFL A;  1W4U A;  2GRP A;  4ONN A;  2BF8 A;  4A4C C;  1JAT A;  4GPR A;  5F6X A;  1I7K A;  3RPG A;  5F6E A;  3EB6 B;  2MT6 A;  3L1Z A;  4Y1L A;  2GRN A; 
#chains in the Genus database with same CATH homology
 4AP4 B;  2FUH A;  4NRI A;  2YB6 A;  3OBU A;  2OXQ A;  2AAK A;  2H2Y A;  2K07 A;  2KLY A;  1FXT A;  4LDT C;  5D1M A;  2KJH A;  3PTF A;  4BVU B;  3O2U A;  2C2V B;  4ONL B;  2O25 A;  1FZY A;  3R3Q A;  2UCZ A;  2AYV A;  2PX9 B;  3FSH A;  2ONU A;  3K9O A;  5AIT D;  2C2V C;  1M4Q A;  5EGG A;  4NR3 B;  4NRG B;  3KPA A;  1X23 A;  1J7D B;  3VON B;  3CEG A;  3OBS A;  1Z3D A;  1J7D A;  4V3L A;  5IFR A;  2DAY A;  4YII U;  1KPQ A;  2OB4 A;  2E2C A;  1Z5S A;  5D1K A;  3FN1 B;  5FER B;  2PWQ A;  2F4W A;  5D0M A;  1YH2 A;  3BZH A;  4DHZ F;  3VON C;  4QPL B;  4Q5E C;  2Z6O A;  2AWF A;  3OBX A;  1S1Q A;  3F92 A;  1U9B A;  2C4P A;  2YBF A;  4M1N A;  4DHJ C;  3SQV C;  1YLA A;  1U9A A;  2Z6P A;  5AIE B;  3UIP A;  4II2 C;  2EBK A;  1Y8X A;  2EKE A;  3H8K A;  4S3O A;  5D2M A;  1PZV A;  4ONL A;  4DHI D;  3HCU B;  4EJE A;  3SY2 C;  2CLW B;  1WZW A;  4JUE A;  2NVU C;  5HPT C;  5F6V A;  4DS2 A;  4DDG A;  1FBV C;  1ZUO A;  1J74 A;  1QCQ A;  1ZDN A;  2ESK A;  1Y6L A;  1AYZ A;  3OJ4 A;  2EDI A;  4NRG A;  4NR3 A;  3RZ3 A;  1TTE A;  2GMI B;  3L1Y A;  5JNE B;  1KPS A;  2Z5D A;  2GRQ A;  2YHO B;  4FH1 A;  2LXP A;  1Q34 A;  3ONG B;  3ZQS A;  1C4Z D;  2F4Z A;  4YC1 A;  3OBQ A;  1UKX A;  4A49 B;  5F6W A;  1M4P A;  3ZNI C;  2YZ0 A;  1A3S A;  4IP3 B;  2EBM A;  4CCG A;  4V3K A;  2DAX A;  4W5V A;  2F0R A;  4ONM B;  1JBB A;  3A4S A;  3UIO A;  4Q5H C;  5F6D A;  3RCZ B;  2UYZ A;  4R62 A;  4WZ3 A;  4A4B C;  1JAS A;  4ONN B;  1YRV A;  4P5O G;  4TKP A;  2BEP A;  2CLW A;  3WE5 A;  1JAT B;  2Y9P A;  2QGX A;  2FO3 A;  4ZNY A;  5KNL C;  2XWU A;  2DAW A;  5D1L A;  3HCT B;  3E95 C;  3JW0 A;  5AIU B;  1KPP A;  2CYX A;  4NRI B;  5F6U A;  2R0J A;  3UGB A;  2PE6 A;  2Y4W A;  1UZX A;  2GMI A;  4AUQ A;  2VRR A;  3EVX A;  1Z2U A;  1WZV A;  3R42 A;  4L83 A;  4Y1L C;  3W31 B;  2GRR A;  3JVZ A;  4MDK A;  1ZGU A;  2ESQ A;  2ESP A;  5F6Y A;  4BWF A;  3K9P A;  2GRO A;  2Q0V A;  2A4D A;  5D0K A;  5FQ2 A;  2Y9M A;  5AIT B;  4DDI A;  3TGD A;  3P9H A;  2HLW A;  2GJD A;  2A7L A;  2ESO A;  4ONM A;  2DMF A;  3P9G A;  4X57 A;  2O25 C;  4JQU A;  3UIN A;  4LAD A;  3E46 A;  3E95 A;  1YF9 A;  3A33 A;  5DFL A;  1W4U A;  2GRP A;  4ONN A;  2BF8 A;  4A4C C;  1JAT A;  4GPR A;  5F6X A;  1I7K A;  3RPG A;  5F6E A;  3EB6 B;  2MT6 A;  3L1Z A;  4Y1L A;  2GRN 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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5D1MA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations