3IRTA

Crystal structure of the i93m mutant of ubiquitin carboxy-terminal hydrolase l1
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 5-220 216 1-4, 221-223 4 3 knot
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-31 6-162 157 1-5 217-223 163-216 5 7 slipknot
Chain Sequence
MQLKPMEINPEMLNKVLSRLGVAGQWRFVDVLGLEEESLGSVPAPACALLLLFPLTAQHENFRKKQIEELKGQEVSPKVYFMKQTIGNSCGTMGLIHAVANNQDKLGFEDGSVLKQFLSETEKMSPEDRAKCFEKNEAIQAAHDAVAQEGQCRVDDKVNFHFILFNNVDGHLYELDGRMPFPVNHGASSEDTLLKDAAKVCREFTEREQGEVRFSAVALCKAA
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 5-220 216 1-4, 221-223 4 3 knot
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1.1m 5-161 157 1-4 165-223 162-164 4 59 slipknot
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2.1m 8-164 157 1-7 170-223 165-169 7 54 slipknot
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2.1m 4-173 170 1-3 180-223 174-179 3 44 slipknot
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3.1m 8-183 176 1-7 197-223 184-196 7 27 slipknot
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3.1m 5-196 192 1-4 203-223 197-202 4 21 slipknot
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3.1m 8-197 190 1-7 217-223 198-216 7 7 slipknot
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3.1m 5-216 212 1-4 218-223 217-217 4 6 slipknot
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2.1m 7-181 175 1-2, 184-223 3-6, 182-183 2 40 slipknot
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2.1m 10-197 188 1-7, 215-223 8-9, 198-214 7 9 slipknot
sequence length 223
structure length 223
publication title Ubiquitin vinyl methyl ester binding orients the misaligned active site of the ubiquitin hydrolase UCHL1 into productive conformation.
pubmed doi rcsb
molecule tags Hydrolase, ligase
molecule keywords Ubiquitin carboxyl-terminal hydrolase isozyme L1
source organism Homo sapiens
total genus Genus: 67
ec nomenclature ec 3.4.19.12: Ubiquitinyl hydrolase 1.
pdb deposition date 2009-08-24
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 3irtA00
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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#similar chains in the pdb database (?% sequence similarity)
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