5FER | Genus

Total Genus 41

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	41
sequence length	145
structure length	145
Chain Sequence	MALKRIQKELSDLQRDPPAHCRAGPVGDDLFHWQATIMGPPDSAYQGGVFFLTVHFPTDYPFKPPKIAFTTKIYHPNINSNGSIKLDILRSQWSPALTVSKVLLSICSLLCDPNPDDPLVPDIAQIYKSDKEKYNRHAREWTQKY

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/5d0d8b81970529d909d8008b/pdb.gz

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The Resolver thinks Pdb

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

Time for openFile(/file/5d0d8b81970529d909d8008b/pdb.gz): 1320 ms

reading 145 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

145 atoms created

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

Time for creating model: 18 ms

Adding embedded #jmolscript: select ({0:144});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	Functional role of TRIM E3 ligase oligomerization and regulation of catalytic activity. pubmed doi rcsb
molecule keywords	E3 ubiquitin/ISG15 ligase TRIM25
total genus	41
structure length	145
sequence length	145
chains with identical sequence	E
ec nomenclature	ec 2.3.2.23: E2 ubiquitin-conjugating enzyme.
pdb deposition date	2015-12-17

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
B	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	5ferB00

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

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

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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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5FERB

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations