3IFWA

Crystal structure of the s18y variant of ubiquitin carboxy terminal hydrolase l1 bound to ubiquitin vinylmethylester.
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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-31 5-164 160 1-4 218-223 165-217 4 6 slipknot
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-52 5-220 216 1-4, 221-223 4 3 knot
Chain Sequence
MQLKPMEINPEMLNKVLYRLGVAGQWRFVDVLGLEEESLGSVPAPACALLLLFPLTAQHENFRKKQIEELKGQEVSPKVYFMKQTIGNSCGTIGLIHAVANNQDKLGFEDGSVLKQFLSETEKMSPEDRAKCFEKNEAIQAAHDAVAQEGQCRVDDKVNFHFILFNNVDGHLYELDGRMPFPVNHGASSEDTLLKDAAKVCREFTEREQGEVRFSAVALCKAA
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 4-220 217 1-3, 221-223 3 3 knot
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2.1m 6-163 158 1-5 171-223 164-170 5 53 slipknot
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3.1m 4-170 167 1-3 174-223 171-173 3 50 slipknot
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2.1m 5-179 175 1-4 187-223 180-186 4 37 slipknot
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3.1m 8-185 178 1-7 191-223 186-190 7 33 slipknot
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2.1m 8-190 183 1-7 193-223 191-192 7 31 slipknot
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3.1m 5-192 188 1-4 210-223 193-209 4 14 slipknot
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2.1m 8-203 196 1-7 215-223 204-214 7 9 slipknot
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3.1m 5-214 210 1-4 218-223 215-217 4 6 slipknot
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2.1m 7-200 194 1-4, 203-223 5-6, 201-202 4 21 slipknot
publication title Ubiquitin vinyl methyl ester binding orients the misaligned active site of the ubiquitin hydrolase UCHL1 into productive conformation.
pubmed doi rcsb
structure length 223
molecule tags Hydrolase/hydrolase inhibitor
source organism Homo sapiens
sequence length 223
molecule keywords Ubiquitin carboxyl-terminal hydrolase isozyme L1
ec nomenclature ec 3.4.19.12: Ubiquitinyl hydrolase 1.
pdb deposition date 2009-07-26
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 3ifwA00
3KW5A 3IHRA 3RIIA 4DM9A 3RISA 3IFWA 2ETLA 1CMXA 3KVFA 2LENA 3A7SA 1XD3A 1UCHA 3IRTA
chains in the KnotProt database with same CATH superfamily
3KW5A 3IHRA 3RIIA 4DM9A 3RISA 3IFWA 2ETLA 1CMXA 3KVFA 2LENA 3A7SA 1XD3A 1UCHA 3IRTA
chains in the KnotProt database with same CATH topology
3KW5A 3IHRA 3RIIA 4DM9A 3RISA 3IFWA 2ETLA 1CMXA 3KVFA 2LENA 3A7SA 1XD3A 1UCHA 3IRTA
chains in the KnotProt database with same CATH homology


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