4DM9A

The crystal structure of ubiquitin carboxy-terminal hydrolase l1 (uchl1) bound to a tripeptide fluoromethyl ketone z-vae(ome)-fmk
Knot K -52 -31 -31
Knot core range Knot core length Knot tails range Slipknot tails range Slipknot loops range N-end length C-end length Type
view details
-52 5-219 215 1-4, 220-223 4 4 knot
view details
-31 6-164 159 1-5 217-223 165-216 5 7 slipknot
Chain Sequence
MQLKPMEINPEMLNKVLSRLGVAGQWRFVDVLGLEEESLGSVPAPACALLLLFPLTAQHENFRKKQIEELKGQEVSPKVYFMKQTIGNSCGTIGLIHAVANNQDKLGFEDGSVLKQFLSETEKMSPEDRAKCFEKNEAIQAAHDAVAQEGQCRVDDKVNFHFILFNNVDGHLYELDGRMPFPVNHGASSEDTLLKDAAKVCREFTEREQGEVRFSAVALCKAA
Whole chain analysis
Subchain analysis 

Knotoid cutoff: 0.5


Knotoid matrix content: 1

Knot core range Knot core length Knot tails range Slipknot tails range Slipknot loops range N-end length C-end length Type
view details
5.2m 5-219 215 1-4, 220-223 4 4 knot
view details
2.1m 7-163 157 1-6 174-223 164-173 6 50 slipknot
view details
3.1m 6-185 180 1-5 194-223 186-193 5 30 slipknot
view details
3.1m 5-194 190 1-4 218-223 195-217 4 6 slipknot
view details
2.1m 9-183 175 1-2, 196-223 3-8, 184-195 2 28 slipknot
view details
2.1m 7-195 189 1-4, 200-223 5-6, 196-199 4 24 slipknot
view details
3.1m 9-200 192 1-4, 215-223 5-8, 201-214 4 9 slipknot
view details
3.1m 8-196 189 1-6, 199-223 7-7, 197-198 6 25 slipknot
sequence length 223
structure length 223
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
molecule tags Hydrolase, ligase/inhibitor
molecule keywords Ubiquitin carboxyl-terminal hydrolase isozyme L1
source organism Homo sapiens
total genus Genus: 75
ec nomenclature ec 3.4.19.12: Ubiquitinyl hydrolase 1.
pdb deposition date 2012-02-07
KnotProt deposition date 2014-07-31

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 Ubiquitin C-terminal Hydrolase Uch-l3 4dm9A00
3IHRA 3KVFA 3A7SA 1XD3A 2LENA 3IFWA 2ETLA 3IRTA 4DM9A 3KW5A 1UCHA 3RISA 1CMXA 3RIIA
chains in the KnotProt database with same CATH superfamily
3IHRA 3KVFA 3A7SA 1XD3A 2LENA 3IFWA 2ETLA 3IRTA 4DM9A 3KW5A 1UCHA 3RISA 1CMXA 3RIIA
chains in the KnotProt database with same CATH topology
3IHRA 3KVFA 3A7SA 1XD3A 2LENA 3IFWA 2ETLA 3IRTA 4DM9A 3KW5A 1UCHA 3RISA 1CMXA 3RIIA
chains in the KnotProt database with same CATH homology


 
#chains in the KnotProt database with same CATH superfamily
 3IHR A;  3KVF A;  3A7S A;  1XD3 A;  2LEN A;  3IFW A;  2ETL A;  3IRT A;  4DM9 A;  3KW5 A;  1UCH A;  3RIS A;  1CMX A;  3RII A; 
#chains in the KnotProt database with same CATH topology
 3IHR A;  3KVF A;  3A7S A;  1XD3 A;  2LEN A;  3IFW A;  2ETL A;  3IRT A;  4DM9 A;  3KW5 A;  1UCH A;  3RIS A;  1CMX A;  3RII A; 
#chains in the KnotProt database with same CATH homology
 3IHR A;  3KVF A;  3A7S A;  1XD3 A;  2LEN A;  3IFW A;  2ETL A;  3IRT A;  4DM9 A;  3KW5 A;  1UCH A;  3RIS A;  1CMX A;  3RII A; 
...loading similar chains, please wait...
similar chains in the KnotProt database (?% sequence similarity)
...loading similar chains, please wait...
similar chains in the pdb database (?% sequence similarity)

 
#similar chains in the KnotProt database (?% sequence similarity)
...loading similar chains, please wait...
#similar chains, but unknotted
...loading similar chains, please wait...
#similar chains in the pdb database (?% sequence similarity)
...loading similar chains, please wait...

KnotProt | Interdisciplinary Laboratory of Biological Systems Modelling