3KVFA

Crystal structure of the i93m mutant 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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-52 5-219 215 1-4, 220-223 4 4 knot
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-31 6-164 159 1-5 218-223 165-217 5 6 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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3.1m 6-165 160 1-5 177-223 166-176 5 47 slipknot
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2.1m 7-179 173 1-6 185-223 180-184 6 39 slipknot
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3.1m 5-184 180 1-4 196-223 185-195 4 28 slipknot
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3.1m 6-184 179 1-4, 194-223 5-5, 185-193 4 30 slipknot
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2.1m 8-201 194 1-7 215-223 202-214 7 9 slipknot
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3.1m 7-184 178 1-5, 193-223 6-6, 185-192 5 31 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/signaling protein
molecule keywords Ubiquitin carboxyl-terminal hydrolase isozyme L1
source organism Homo sapiens
total genus Genus: 62
ec nomenclature ec 3.4.19.12: Ubiquitinyl hydrolase 1.
pdb deposition date 2009-11-30
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 3kvfA00
1XD3A 3RIIA 2LENA 3A7SA 3RISA 3IHRA 3KVFA 3IFWA 2ETLA 4DM9A 3KW5A 1CMXA 1UCHA 3IRTA
chains in the KnotProt database with same CATH superfamily
1XD3A 3RIIA 2LENA 3A7SA 3RISA 3IHRA 3KVFA 3IFWA 2ETLA 4DM9A 3KW5A 1CMXA 1UCHA 3IRTA
chains in the KnotProt database with same CATH topology
1XD3A 3RIIA 2LENA 3A7SA 3RISA 3IHRA 3KVFA 3IFWA 2ETLA 4DM9A 3KW5A 1CMXA 1UCHA 3IRTA
chains in the KnotProt database with same CATH homology


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

 
#similar chains in the KnotProt 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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