4JWG | Genus

Total Genus 67

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	67
Knots found	KnotProt 2.0: K +3₁
sequence length	187
structure length	187
Chain Sequence	RIRLGKVVPSSIRIVLDCAFDDLMNDKEINSLCQQVTRCHSANRTALHPVELFATNFGGRLKTRQDFVLKGQQNNWKRYNPTTKSYLEEFESQKEKLVYLSADSDNTITELDEDKIYIIGAIVDKNRYKNLCQNKASEQGIKTAKLPIDEYIKITDRKILTVNQVFEILSLWLEYRDWEKAFMEVIP

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/5d00607cbb1c97f61f5c845b/pdb.gz): 1956 ms

reading 187 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

187 atoms created

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

Time for creating model: 27 ms

Adding embedded #jmolscript: select ({0:186});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

publication title	Crystal structure of tRNA m1G9 methyltransferase Trm10: insight into the catalytic mechanism and recognition of tRNA substrate. pubmed doi rcsb
molecule keywords	tRNA (guanine(9)-N1)-methyltransferase
molecule tags	Transferase
source organism	Schizosaccharomyces pombe
total genus	67
structure length	187
sequence length	187
other databases	KnotProt 2.0: K +3₁
ec nomenclature	ec 2.1.1.221: tRNA (guanine(9)-N(1))-methyltransferase.
pdb deposition date	2013-03-27

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF01746	tRNA_m1G_MT	tRNA (Guanine-1)-methyltransferase

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

cath code	Class	Architecture	Topology	Homology	Domain
3.40.1280.30	Alpha Beta	3-Layer(aba) Sandwich	Alpha/beta knot	Alpha/beta knot	4jwgA00

4JWFA 4JWGA 4JWHA 4JWJA 4FMWA
chains in the Genus database with same CATH superfamily

1VH0A 4YQ8A 1NXZA 2QMMA 4YQ1A 4YQ3A 3NK6A 4YQJA 4JWHA 4YQ0A 3AI9X 3L8UA 3OIIA 4XBOA 4MCBA 2YY8A 3BBHA 4YPZA 3AIAA 4MCDA 3KNUA 3DCMX 4CNGA 5GM8A 3OINA 1OY5A 4YQKA 4MCCA 2V3JA 1V2XA 4CNDA 4YVGA 4JWFA 2CX8A 4YQAA 4X3MA 4FAKA 3ONPA 3O7BA 1UAJA 1GZ0A 4YPXA 2QWVA 4YQ7A 3AXZA 2O3AA 4J3CA 3NK7A 4FMWA 4YQ6A 1NS5A 3GYQA 3KY7A 1UALA 5CO4A 2I6DA 3E5YA 1MXIA 4CNEA 3OIJA 3KW2A 5GMBA 1VHKA 4YQNA 4YQPA 4YQBA 3N4KA 4KDZA 4YQOA 5GMCA 5D9FA 4CNFA 4YQ9A 3IEFA 1O6DA 4PZKA 1V6ZA 4L69A 4X3LA 4YQIA 4JALA 2HA8A 4JWGA 4YVHA 4YQ4A 4YQCA 1UAKA 3IC6A 4RG1A 5FAIA 4E8BA 4YQTA 1X7OA 4YPWA 4YQLA 3ILKA 4YVJA 4JWJA 3BBDA 1P9PA 4H3YA 1X7PA 1UAMA 2EGVA 1K3RA 4H3ZA 3N4JA 4YVKA 1ZJRA 4YQGA 1Z85A 1VHYA 4YQDA 3QUVA 2EGWA 4JAKA 1IPAA 3KTYA 4YVIA 4YQRA 2Z0YA 4YQQA 4YQSA 2V3KA 4YPYA 1J85A 4YQ5A 3BBEA 4IG6A 1TO0A 4YQ2A 4KGNA
chains in the Genus database with same CATH topology

#chains in the Genus database with same CATH superfamily
 4JWF A;  4JWG A;  4JWH A;  4JWJ A;  4FMW A; 
#chains in the Genus database with same CATH topology
 1VH0 A;  4YQ8 A;  1NXZ A;  2QMM A;  4YQ1 A;  4YQ3 A;  3NK6 A;  4YQJ A;  4JWH A;  4YQ0 A;  3AI9 X;  3L8U A;  3OII A;  4XBO A;  4MCB A;  2YY8 A;  3BBH A;  4YPZ A;  3AIA A;  4MCD A;  3KNU A;  3DCM X;  4CNG A;  5GM8 A;  3OIN A;  1OY5 A;  4YQK A;  4MCC A;  2V3J A;  1V2X A;  4CND A;  4YVG A;  4JWF A;  2CX8 A;  4YQA A;  4X3M A;  4FAK A;  3ONP A;  3O7B A;  1UAJ A;  1GZ0 A;  4YPX A;  2QWV A;  4YQ7 A;  3AXZ A;  2O3A A;  4J3C A;  3NK7 A;  4FMW A;  4YQ6 A;  1NS5 A;  3GYQ A;  3KY7 A;  1UAL A;  5CO4 A;  2I6D A;  3E5Y A;  1MXI A;  4CNE A;  3OIJ A;  3KW2 A;  5GMB A;  1VHK A;  4YQN A;  4YQP A;  4YQB A;  3N4K A;  4KDZ A;  4YQO A;  5GMC A;  5D9F A;  4CNF A;  4YQ9 A;  3IEF A;  1O6D A;  4PZK A;  1V6Z A;  4L69 A;  4X3L A;  4YQI A;  4JAL A;  2HA8 A;  4JWG A;  4YVH A;  4YQ4 A;  4YQC A;  1UAK A;  3IC6 A;  4RG1 A;  5FAI A;  4E8B A;  4YQT A;  1X7O A;  4YPW A;  4YQL A;  3ILK A;  4YVJ A;  4JWJ A;  3BBD A;  1P9P A;  4H3Y A;  1X7P A;  1UAM A;  2EGV A;  1K3R A;  4H3Z A;  3N4J A;  4YVK A;  1ZJR A;  4YQG A;  1Z85 A;  1VHY A;  4YQD A;  3QUV A;  2EGW A;  4JAK A;  1IPA A;  3KTY A;  4YVI A;  4YQR A;  2Z0Y A;  4YQQ A;  4YQS A;  2V3K A;  4YPY A;  1J85 A;  4YQ5 A;  3BBE A;  4IG6 A;  1TO0 A;  4YQ2 A;  4KGN A; 
#chains in the Genus database with same CATH homology
 1VH0 A;  4YQ8 A;  1NXZ A;  2QMM A;  4YQ1 A;  4YQ3 A;  3NK6 A;  4YQJ A;  4JWH A;  4YQ0 A;  3AI9 X;  3L8U A;  3OII A;  4XBO A;  4MCB A;  2YY8 A;  3BBH A;  4YPZ A;  3AIA A;  4MCD A;  3KNU A;  3DCM X;  4CNG A;  5GM8 A;  3OIN A;  1OY5 A;  4YQK A;  4MCC A;  2V3J A;  1V2X A;  4CND A;  4YVG A;  4JWF A;  2CX8 A;  4YQA A;  4X3M A;  4FAK A;  3ONP A;  3O7B A;  1UAJ A;  1GZ0 A;  4YPX A;  2QWV A;  4YQ7 A;  3AXZ A;  2O3A A;  4J3C A;  3NK7 A;  4FMW A;  4YQ6 A;  1NS5 A;  3GYQ A;  3KY7 A;  1UAL A;  5CO4 A;  2I6D A;  3E5Y A;  1MXI A;  4CNE A;  3OIJ A;  3KW2 A;  5GMB A;  1VHK A;  4YQN A;  4YQP A;  4YQB A;  3N4K A;  4KDZ A;  4YQO A;  5GMC A;  5D9F A;  4CNF A;  4YQ9 A;  3IEF A;  1O6D A;  4PZK A;  1V6Z A;  4L69 A;  4X3L A;  4YQI A;  4JAL A;  2HA8 A;  4JWG A;  4YVH A;  4YQ4 A;  4YQC A;  1UAK A;  3IC6 A;  4RG1 A;  5FAI A;  4E8B A;  4YQT A;  1X7O A;  4YPW A;  4YQL A;  3ILK A;  4YVJ A;  4JWJ A;  3BBD A;  1P9P A;  4H3Y A;  1X7P A;  1UAM A;  2EGV A;  1K3R A;  4H3Z A;  3N4J A;  4YVK A;  1ZJR A;  4YQG A;  1Z85 A;  1VHY A;  4YQD A;  3QUV A;  2EGW A;  4JAK A;  1IPA A;  3KTY A;  4YVI A;  4YQR A;  2Z0Y A;  4YQQ A;  4YQS A;  2V3K A;  4YPY A;  1J85 A;  4YQ5 A;  3BBE A;  4IG6 A;  1TO0 A;  4YQ2 A;  4KGN 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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#similar chains in the pdb database (?% sequence similarity)
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4JWGA

Total Genus

Knots found

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations