Structure of PDB 3kvf Chain A Binding Site BS01

Receptor Information
>3kvf Chain A (length=223) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MQLKPMEINPEMLNKVLSRLGVAGQWRFVDVLGLEEESLGSVPAPACALL
LLFPLTAQHENFRKKQIEELKGQEVSPKVYFMKQTIGNSCGTMGLIHAVA
NNQDKLGFEDGSVLKQFLSETEKMSPEDRAKCFEKNEAIQAAHDAVAQEG
QCRVDDKVNFHFILFNNVDGHLYELDGRMPFPVNHGASSEDTLLKDAAKV
CREFTEREQGEVRFSAVALCKAA
Ligand information
Ligand IDGVE
InChIInChI=1S/C5H11NO2/c1-8-5(7)3-2-4-6/h2-4,6H2,1H3
InChIKeyKVQGGLZHHFGHPU-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.370
OpenEye OEToolkits 1.7.0		COC(=O)CCCN
ACDLabs 12.01O=C(OC)CCCN
FormulaC5 H11 N O2
NameMETHYL 4-AMINOBUTANOATE
ChEMBL
DrugBank
ZINCZINC000002019854
PDB chain3kvf Chain B Residue 76 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB3kvf Ubiquitin vinyl methyl ester binding orients the misaligned active site of the ubiquitin hydrolase UCHL1 into productive conformation.
Resolution2.8 Å
Binding residue
(original residue number in PDB)		Q84 N88 C90 F160
Binding residue
(residue number reindexed from 1)		Q84 N88 C90 F160
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) Q84 C90 H161 D176
Catalytic site (residue number reindexed from 1) Q84 C90 H161 D176
Enzyme Commision number 3.4.19.12: ubiquitinyl hydrolase 1.
Gene Ontology
Molecular Function
GO:0004197 cysteine-type endopeptidase activity
GO:0004843 cysteine-type deubiquitinase activity
GO:0005515 protein binding
GO:0008234 cysteine-type peptidase activity
GO:0008242 omega peptidase activity
GO:0031625 ubiquitin protein ligase binding
GO:0031694 alpha-2A adrenergic receptor binding
GO:0043022 ribosome binding
GO:0043130 ubiquitin binding
Biological Process
GO:0002176 male germ cell proliferation
GO:0002931 response to ischemia
GO:0006508 proteolysis
GO:0006511 ubiquitin-dependent protein catabolic process
GO:0007409 axonogenesis
GO:0007412 axon target recognition
GO:0007628 adult walking behavior
GO:0016241 regulation of macroautophagy
GO:0016579 protein deubiquitination
GO:0019896 axonal transport of mitochondrion
GO:0042755 eating behavior
GO:0043161 proteasome-mediated ubiquitin-dependent protein catabolic process
GO:0043407 negative regulation of MAP kinase activity
GO:0045821 positive regulation of glycolytic process
GO:0050905 neuromuscular process
GO:0055001 muscle cell development
GO:0071466 cellular response to xenobiotic stimulus
Cellular Component
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0030424 axon
GO:0043025 neuronal cell body
GO:0044306 neuron projection terminus
GO:1904115 axon cytoplasm

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3kvf, PDBe:3kvf, PDBj:3kvf
PDBsum3kvf
PubMed20439756
UniProtP09936|UCHL1_HUMAN Ubiquitin carboxyl-terminal hydrolase isozyme L1 (Gene Name=UCHL1)

[Back to BioLiP]