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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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
molecule tags Hydrolase, ligase/inhibitor
molecule keywords Ubiquitin carboxyl-terminal hydrolase isozyme L1
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
3TB3A 4JKJA 4IG7A 1XD3A 3IFWA 3IRTA 4UELA 3RIIA 1CMXA 4DM9A 3IHRA 3KVFA 3RISA 3KW5A 1UCHA 3A7SA 4UEMA 4I6NA 2LENA 2ETLA
chains in the Genus database with same CATH superfamily
3TB3A 4JKJA 4IG7A 1XD3A 3IFWA 3IRTA 4UELA 3RIIA 1CMXA 4DM9A 3IHRA 3KVFA 3RISA 3KW5A 1UCHA 3A7SA 4UEMA 4I6NA 2LENA 2ETLA
chains in the Genus database with same CATH topology
3TB3A 4JKJA 4IG7A 1XD3A 3IFWA 3IRTA 4UELA 3RIIA 1CMXA 4DM9A 3IHRA 3KVFA 3RISA 3KW5A 1UCHA 3A7SA 4UEMA 4I6NA 2LENA 2ETLA
chains in the Genus database with same CATH homology


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