1F5X | Genus

Total Genus 52

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	52
sequence length	208
structure length	208
Chain Sequence	MKGDEIYEDLMRLESVPTPPKMTEYDKRCCCLREIQQTEEKYTDTLGSIQQHFMKPLQRFLKPQDMETIFVNIEELFSVHTHFLKELKDALAGPGATTLYQVFIKYKERFLVYGRYCSQVESASKHLDQVATAREDVQMKLEECSQRANNGRFTLRDLLMVPMQRVLKYHLLLQELVKHTQDATEKENLRLALDAMRDLAQCVNEVKR

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/5d29abfee0498bc1a29f3abe/pdb.gz): 1590 ms

reading 208 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

208 atoms created

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

Time for creating model: 32 ms

Adding embedded #jmolscript: select ({0:207});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	Signaling protein
source organism	Mus musculus
publication title	Structural basis for relief of autoinhibition of the Dbl homology domain of proto-oncogene Vav by tyrosine phosphorylation. pubmed doi rcsb
molecule keywords	RHO-GEF VAV
total genus	52
structure length	208
sequence length	208
ec nomenclature
pdb deposition date	2000-06-18

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF00621	RhoGEF	RhoGEF domain

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

cath code	Class	Architecture	Topology	Homology	Domain
1.20.900.10	Mainly Alpha	Up-down Bundle	Dbl Homology Domain; Chain A	Dbl homology (DH) domain	1f5xA00

1F5XA 2KR9A 3ODXA 4GYVA 1XCGA 3JV3A 3EO2A 3GF9A 2Z0QA 2DX1A 4D0NB 2PZ1A 3QBVB 3ODOA 1X86A 2NZ8B 4YONA 3ODWA 3KSYA 3BJIA 5FI1A 3KZ1A 3T06A 5FI0A 1XD4A 2VRWB 4MT7A 1KI1B 5JHGA 5JHHA 1DBHA 1RJ2A 1LB1A 3KY9A 4D0OA 2RGNB 1KZ7A 1FOEA 1KZGA 1TXDA 2DFKA 1BY1A 3P6AA 4GZUA 1NTYA 4GOUA 3MPXA
chains in the Genus database with same CATH superfamily

#chains in the Genus database with same CATH superfamily
 1F5X A;  2KR9 A;  3ODX A;  4GYV A;  1XCG A;  3JV3 A;  3EO2 A;  3GF9 A;  2Z0Q A;  2DX1 A;  4D0N B;  2PZ1 A;  3QBV B;  3ODO A;  1X86 A;  2NZ8 B;  4YON A;  3ODW A;  3KSY A;  3BJI A;  5FI1 A;  3KZ1 A;  3T06 A;  5FI0 A;  1XD4 A;  2VRW B;  4MT7 A;  1KI1 B;  5JHG A;  5JHH A;  1DBH A;  1RJ2 A;  1LB1 A;  3KY9 A;  4D0O A;  2RGN B;  1KZ7 A;  1FOE A;  1KZG A;  1TXD A;  2DFK A;  1BY1 A;  3P6A A;  4GZU A;  1NTY A;  4GOU A;  3MPX A; 
#chains in the Genus database with same CATH topology
 1F5X A;  2KR9 A;  3ODX A;  4GYV A;  1XCG A;  3JV3 A;  3EO2 A;  3GF9 A;  2Z0Q A;  2DX1 A;  4D0N B;  2PZ1 A;  3QBV B;  3ODO A;  1X86 A;  2NZ8 B;  4YON A;  3ODW A;  3KSY A;  3BJI A;  5FI1 A;  3KZ1 A;  3T06 A;  5FI0 A;  1XD4 A;  2VRW B;  4MT7 A;  1KI1 B;  5JHG A;  5JHH A;  1DBH A;  1RJ2 A;  1LB1 A;  3KY9 A;  4D0O A;  2RGN B;  1KZ7 A;  1FOE A;  1KZG A;  1TXD A;  2DFK A;  1BY1 A;  3P6A A;  4GZU A;  1NTY A;  4GOU A;  3MPX A; 
#chains in the Genus database with same CATH homology
 1F5X A;  2KR9 A;  3ODX A;  4GYV A;  1XCG A;  3JV3 A;  3EO2 A;  3GF9 A;  2Z0Q A;  2DX1 A;  4D0N B;  2PZ1 A;  3QBV B;  3ODO A;  1X86 A;  2NZ8 B;  4YON A;  3ODW A;  3KSY A;  3BJI A;  5FI1 A;  3KZ1 A;  3T06 A;  5FI0 A;  1XD4 A;  2VRW B;  4MT7 A;  1KI1 B;  5JHG A;  5JHH A;  1DBH A;  1RJ2 A;  1LB1 A;  3KY9 A;  4D0O A;  2RGN B;  1KZ7 A;  1FOE A;  1KZG A;  1TXD A;  2DFK A;  1BY1 A;  3P6A A;  4GZU A;  1NTY A;  4GOU A;  3MPX 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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1F5XA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations