1XD3 | Genus

Total Genus 81

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	81
Knots found	KnotProt 2.0: K -5₂ -3₁ -3₁
sequence length	229
structure length	229
Chain Sequence	EGQRWLPLEANPEVTNQFLKQLGLHPNWQFVDVYGMDPELLSMVPRPVCAVLLLFPITEKYEVFRTEEEEKIKSQGQDVTSSVYFMKQTISNACGTIGLIHAIANNKDKMHFESGSTLKKFLEESVSMSPEERARYLENYDAIRVTHETSAHEGQTEAPSIDEKVDLHFIALVHVDGHLYELDGRKPFPINHGETSDETLLEDAIEVCKKFMERDPDELRFNAIALSAA

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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reading 229 atoms

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229 atoms created

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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	Hydrolase
source organism	Homo sapiens
publication title	Structure of the Ubiquitin Hydrolase UCH-L3 Complexed with a Suicide Substrate pubmed doi rcsb
molecule keywords	Ubiquitin Carboxyl-terminal esterase L3
total genus	81
structure length	229
sequence length	229
chains with identical sequence	C
other databases	KnotProt 2.0: K -5₂ -3₁ -3₁
ec nomenclature	ec 3.4.19.12: Ubiquitinyl hydrolase 1.
pdb deposition date	2004-09-03

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF01088	Peptidase_C12	Ubiquitin carboxyl-terminal hydrolase, family 1

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

cath code	Class	Architecture	Topology	Homology	Domain
3.40.532.10	Alpha Beta	3-Layer(aba) Sandwich	Ubiquitin C-terminal Hydrolase UCH-l3	Peptidase C12, ubiquitin carboxyl-terminal hydrolase	1xd3A00

1UCHA 3IRTA 3IHRA 1XD3A 1CMXA 4DM9A 4I6NA 4UELA 4IG7A 3A7SA 4JKJA 3IFWA 3RISA 2LENA 3TB3A 2ETLA 3KVFA 4UEMA 3KW5A 3RIIA
chains in the Genus database with same CATH superfamily

1UCHA 3IRTA 3IHRA 1XD3A 1CMXA 4DM9A 4I6NA 4UELA 4IG7A 3A7SA 4JKJA 3IFWA 3RISA 2LENA 3TB3A 2ETLA 3KVFA 4UEMA 3KW5A 3RIIA
chains in the Genus database with same CATH topology

1UCHA 3IRTA 3IHRA 1XD3A 1CMXA 4DM9A 4I6NA 4UELA 4IG7A 3A7SA 4JKJA 3IFWA 3RISA 2LENA 3TB3A 2ETLA 3KVFA 4UEMA 3KW5A 3RIIA
chains in the Genus database with same CATH homology

#chains in the Genus database with same CATH superfamily
 1UCH A;  3IRT A;  3IHR A;  1XD3 A;  1CMX A;  4DM9 A;  4I6N A;  4UEL A;  4IG7 A;  3A7S A;  4JKJ A;  3IFW A;  3RIS A;  2LEN A;  3TB3 A;  2ETL A;  3KVF A;  4UEM A;  3KW5 A;  3RII A; 
#chains in the Genus database with same CATH topology
 1UCH A;  3IRT A;  3IHR A;  1XD3 A;  1CMX A;  4DM9 A;  4I6N A;  4UEL A;  4IG7 A;  3A7S A;  4JKJ A;  3IFW A;  3RIS A;  2LEN A;  3TB3 A;  2ETL A;  3KVF A;  4UEM A;  3KW5 A;  3RII A; 
#chains in the Genus database with same CATH homology
 1UCH A;  3IRT A;  3IHR A;  1XD3 A;  1CMX A;  4DM9 A;  4I6N A;  4UEL A;  4IG7 A;  3A7S A;  4JKJ A;  3IFW A;  3RIS A;  2LEN A;  3TB3 A;  2ETL A;  3KVF A;  4UEM A;  3KW5 A;  3RII 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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1XD3A

Total Genus

Knots found

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations