4DM9A

The crystal structure of ubiquitin carboxy-terminal hydrolase l1 (uchl1) bound to a tripeptide fluoromethyl ketone z-vae(ome)-fmk
Total Genus 75
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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
75
Knots found
sequence length
223
structure length
223
Chain Sequence
MQLKPMEINPEMLNKVLSRLGVAGQWRFVDVLGLEEESLGSVPAPACALLLLFPLTAQHENFRKKQIEELKGQEVSPKVYFMKQTIGNSCGTIGLIHAVANNQDKLGFEDGSVLKQFLSETEKMSPEDRAKCFEKNEAIQAAHDAVAQEGQCRVDDKVNFHFILFNNVDGHLYELDGRMPFPVNHGASSEDTLLKDAAKVCREFTEREQGEVRFSAVALCKAA
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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

After clicking on a point (x,y) in the genus matrix above, a subchain from x to y is shown in color.

Chord Diagram
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molecule tags Hydrolase, ligase/inhibitor
molecule keywords Ubiquitin carboxyl-terminal hydrolase isozyme L1
publication title The co-crystal structure of ubiquitin carboxy-terminal hydrolase L1 (UCHL1) with a tripeptide fluoromethyl ketone (Z-VAE(OMe)-FMK).
pubmed doi rcsb
source organism Homo sapiens
total genus 75
structure length 223
sequence length 223
chains with identical sequence B
other databases KnotProt 2.0: K -52 -31 -31
ec nomenclature ec 3.4.19.12: Ubiquitinyl hydrolase 1.
pdb deposition date 2012-02-07

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
ClassArchitectureTopologyHomologyDomain
3.40.532.10 Alpha Beta 3-Layer(aba) Sandwich Ubiquitin C-terminal Hydrolase UCH-l3 Peptidase C12, ubiquitin carboxyl-terminal hydrolase 4dm9A00
4DM9A 4UEMA 4IG7A 3A7SA 3IHRA 3RIIA 1UCHA 1CMXA 4JKJA 3TB3A 3IRTA 2LENA 2ETLA 3KVFA 1XD3A 4I6NA 3IFWA 3KW5A 4UELA 3RISA
chains in the Genus database with same CATH superfamily
4DM9A 4UEMA 4IG7A 3A7SA 3IHRA 3RIIA 1UCHA 1CMXA 4JKJA 3TB3A 3IRTA 2LENA 2ETLA 3KVFA 1XD3A 4I6NA 3IFWA 3KW5A 4UELA 3RISA
chains in the Genus database with same CATH topology
4DM9A 4UEMA 4IG7A 3A7SA 3IHRA 3RIIA 1UCHA 1CMXA 4JKJA 3TB3A 3IRTA 2LENA 2ETLA 3KVFA 1XD3A 4I6NA 3IFWA 3KW5A 4UELA 3RISA
chains in the Genus database with same CATH homology


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