5T1X | Genus

Total Genus 28

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	28
sequence length	110
structure length	110
Chain Sequence	NIPFTDNLLFSGQVLYGDGRLTAKNHQLVMQGDCNLVLYGGKYGWQSNTHGNGEHCFLRLNHKGELIIKDDDFKTIWSSNSSSKQGDYVLILRDDGFAVIYGPAIWETSA

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/5d01abf0dd3511e913d61d96/pdb.gz): 2624 ms

reading 110 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

110 atoms created

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

Time for creating model: 19 ms

Adding embedded #jmolscript: select ({0:109});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	Sugar binding protein
publication title	High-resolution crystal structures of Colocasia esculenta tarin lectin. pubmed doi rcsb
molecule keywords	Lectin
total genus	28
structure length	110
sequence length	110
chains with identical sequence	D, F, H
ec nomenclature
pdb deposition date	2016-08-22

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

cath code	Class	Architecture	Topology	Homology	Domain
2.90.10.10	Mainly Beta	Orthogonal Prism	Agglutinin, subunit A	Bulb-type lectin domain	5t1xB00

5T1XB 1NPLA 2D04B 3A0DA 4GC2A 3R0EA 1B2PA 1XD6A 4H3OA 5T20B 5D9ZB 3M7HA 4TKCA 3DZWA 2D04A 5J76A 1JPCA 3MEZB 5T1XA 1MSAA 1BWUD 1XD5A 1BWUQ 4GC1A 1NIVA 5T20A 3M7JA 1KJ1D 5D5GB 5D9ZA 3A0EA 3R0EB 1BWUA 3MEZA 1KJ1A 1BWUP 4PDTA 1DLPA 2DPFA 5J76B 3A0CA 5D5GA
chains in the Genus database with same CATH superfamily

5T1XB 1NPLA 2D04B 3A0DA 4OKCA 4GC2A 3R0EA 4LE7A 1B2PA 1XD6A 4H3OA 5T20B 5D9ZB 3M7HA 4TKCA 3DZWA 2D04A 5J76A 1JPCA 3MEZB 5T1XA 1MSAA 1BWUD 1XD5A 1BWUQ 4GC1A 4OIZA 1NIVA 5T20A 3M7JA 1KJ1D 5D5GB 5D9ZA 3A0EA 3R0EB 1BWUA 3MEZA 4LEDA 4LEAA 4OITA 1KJ1A 1BWUP 4PDTA 1DLPA 2DPFA 5J76B 3A0CA 5D5GA
chains in the Genus database with same CATH topology

#chains in the Genus database with same CATH superfamily
 5T1X B;  1NPL A;  2D04 B;  3A0D A;  4GC2 A;  3R0E A;  1B2P A;  1XD6 A;  4H3O A;  5T20 B;  5D9Z B;  3M7H A;  4TKC A;  3DZW A;  2D04 A;  5J76 A;  1JPC A;  3MEZ B;  5T1X A;  1MSA A;  1BWU D;  1XD5 A;  1BWU Q;  4GC1 A;  1NIV A;  5T20 A;  3M7J A;  1KJ1 D;  5D5G B;  5D9Z A;  3A0E A;  3R0E B;  1BWU A;  3MEZ A;  1KJ1 A;  1BWU P;  4PDT A;  1DLP A;  2DPF A;  5J76 B;  3A0C A;  5D5G A; 
#chains in the Genus database with same CATH topology
 5T1X B;  1NPL A;  2D04 B;  3A0D A;  4OKC A;  4GC2 A;  3R0E A;  4LE7 A;  1B2P A;  1XD6 A;  4H3O A;  5T20 B;  5D9Z B;  3M7H A;  4TKC A;  3DZW A;  2D04 A;  5J76 A;  1JPC A;  3MEZ B;  5T1X A;  1MSA A;  1BWU D;  1XD5 A;  1BWU Q;  4GC1 A;  4OIZ A;  1NIV A;  5T20 A;  3M7J A;  1KJ1 D;  5D5G B;  5D9Z A;  3A0E A;  3R0E B;  1BWU A;  3MEZ A;  4LED A;  4LEA A;  4OIT A;  1KJ1 A;  1BWU P;  4PDT A;  1DLP A;  2DPF A;  5J76 B;  3A0C A;  5D5G A; 
#chains in the Genus database with same CATH homology
 5T1X B;  1NPL A;  2D04 B;  3A0D A;  4GC2 A;  3R0E A;  1B2P A;  1XD6 A;  4H3O A;  5T20 B;  5D9Z B;  3M7H A;  4TKC A;  3DZW A;  2D04 A;  5J76 A;  1JPC A;  3MEZ B;  5T1X A;  1MSA A;  1BWU D;  1XD5 A;  1BWU Q;  4GC1 A;  1NIV A;  5T20 A;  3M7J A;  1KJ1 D;  5D5G B;  5D9Z A;  3A0E A;  3R0E B;  1BWU A;  3MEZ A;  1KJ1 A;  1BWU P;  4PDT A;  1DLP A;  2DPF A;  5J76 B;  3A0C A;  5D5G 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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5T1XB

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN