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
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-52 5-219 215 1-4, 220-223 4 4 knot
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-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
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5.2m 5-219 215 1-4, 220-223 4 4 knot
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2.1m 7-163 157 1-6 174-223 164-173 6 50 slipknot
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3.1m 6-185 180 1-5 194-223 186-193 5 30 slipknot
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3.1m 5-194 190 1-4 218-223 195-217 4 6 slipknot
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2.1m 9-183 175 1-2, 196-223 3-8, 184-195 2 28 slipknot
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2.1m 7-195 189 1-4, 200-223 5-6, 196-199 4 24 slipknot
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3.1m 9-200 192 1-4, 215-223 5-8, 201-214 4 9 slipknot
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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
3IRTA 3IFWA 3RIIA 2ETLA 2LENA 1UCHA 3IHRA 1CMXA 3KVFA 3KW5A 4DM9A 1XD3A 3RISA 3A7SA
chains in the KnotProt database with same CATH superfamily
3IRTA 3IFWA 3RIIA 2ETLA 2LENA 1UCHA 3IHRA 1CMXA 3KVFA 3KW5A 4DM9A 1XD3A 3RISA 3A7SA
chains in the KnotProt database with same CATH topology
3IRTA 3IFWA 3RIIA 2ETLA 2LENA 1UCHA 3IHRA 1CMXA 3KVFA 3KW5A 4DM9A 1XD3A 3RISA 3A7SA
chains in the KnotProt database with same CATH homology


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

 
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#similar chains, but unknotted
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