6QML
UCHL3 in complex with synthetic, K27-linked diubiquitin
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0004843 | molecular_function | cysteine-type deubiquitinase activity |
| A | 0005515 | molecular_function | protein binding |
| A | 0005654 | cellular_component | nucleoplasm |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0005829 | cellular_component | cytosol |
| A | 0006508 | biological_process | proteolysis |
| A | 0006511 | biological_process | ubiquitin-dependent protein catabolic process |
| A | 0008233 | molecular_function | peptidase activity |
| A | 0008234 | molecular_function | cysteine-type peptidase activity |
| A | 0016567 | biological_process | protein ubiquitination |
| A | 0016579 | biological_process | protein deubiquitination |
| A | 0019784 | molecular_function | deNEDDylase activity |
| A | 0030163 | biological_process | protein catabolic process |
| A | 0043130 | molecular_function | ubiquitin binding |
| A | 0043687 | biological_process | post-translational protein modification |
| D | 0004843 | molecular_function | cysteine-type deubiquitinase activity |
| D | 0005515 | molecular_function | protein binding |
| D | 0005654 | cellular_component | nucleoplasm |
| D | 0005737 | cellular_component | cytoplasm |
| D | 0005829 | cellular_component | cytosol |
| D | 0006508 | biological_process | proteolysis |
| D | 0006511 | biological_process | ubiquitin-dependent protein catabolic process |
| D | 0008233 | molecular_function | peptidase activity |
| D | 0008234 | molecular_function | cysteine-type peptidase activity |
| D | 0016567 | biological_process | protein ubiquitination |
| D | 0016579 | biological_process | protein deubiquitination |
| D | 0019784 | molecular_function | deNEDDylase activity |
| D | 0030163 | biological_process | protein catabolic process |
| D | 0043130 | molecular_function | ubiquitin binding |
| D | 0043687 | biological_process | post-translational protein modification |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 4 |
| Details | binding site for residue K A 301 |
| Chain | Residue |
| A | ASN106 |
| A | ASN107 |
| A | HIS175 |
| A | HOH409 |
| site_id | AC2 |
| Number of Residues | 6 |
| Details | binding site for residue EDO A 304 |
| Chain | Residue |
| D | ALA143 |
| A | ASP142 |
| A | EDO307 |
| D | LYS121 |
| D | TYR141 |
| D | ASP142 |
| site_id | AC3 |
| Number of Residues | 5 |
| Details | binding site for residue EDO A 305 |
| Chain | Residue |
| A | ASP33 |
| A | MET44 |
| A | VAL45 |
| A | HOH406 |
| A | HOH458 |
| site_id | AC4 |
| Number of Residues | 4 |
| Details | binding site for residue EDO A 306 |
| Chain | Residue |
| A | GLN30 |
| A | SER228 |
| A | ALA229 |
| A | ALA230 |
| site_id | AC5 |
| Number of Residues | 4 |
| Details | binding site for residue EDO A 307 |
| Chain | Residue |
| A | ASP142 |
| A | ALA143 |
| A | EDO304 |
| D | K303 |
| site_id | AC6 |
| Number of Residues | 1 |
| Details | binding site for residue BR B 101 |
| Chain | Residue |
| B | GLU16 |
| site_id | AC7 |
| Number of Residues | 4 |
| Details | binding site for residue EDO B 102 |
| Chain | Residue |
| A | MET213 |
| A | PRO217 |
| B | THR9 |
| B | HOH210 |
| site_id | AC8 |
| Number of Residues | 5 |
| Details | binding site for residue EDO B 103 |
| Chain | Residue |
| A | GLU40 |
| B | ILE44 |
| B | ALA46 |
| B | GLY47 |
| B | HIS68 |
| site_id | AC9 |
| Number of Residues | 1 |
| Details | binding site for residue BR C 101 |
| Chain | Residue |
| C | GLY75 |
| site_id | AD1 |
| Number of Residues | 4 |
| Details | binding site for residue EDO C 102 |
| Chain | Residue |
| C | LEU15 |
| C | GLU16 |
| C | LYS29 |
| C | LYS33 |
| site_id | AD2 |
| Number of Residues | 4 |
| Details | binding site for residue EDO C 103 |
| Chain | Residue |
| C | LYS6 |
| C | HIS68 |
| C | HOH214 |
| D | GLY116 |
| site_id | AD3 |
| Number of Residues | 4 |
| Details | binding site for residue EDO C 104 |
| Chain | Residue |
| C | THR7 |
| C | LEU8 |
| C | LEU69 |
| C | LEU71 |
| site_id | AD4 |
| Number of Residues | 4 |
| Details | binding site for residue K D 301 |
| Chain | Residue |
| D | ASN106 |
| D | ASN107 |
| D | HIS175 |
| D | HOH414 |
| site_id | AD5 |
| Number of Residues | 6 |
| Details | binding site for residue K D 302 |
| Chain | Residue |
| A | ASN140 |
| A | ASP142 |
| A | HOH478 |
| D | ASN140 |
| D | ASP142 |
| D | HOH449 |
| site_id | AD6 |
| Number of Residues | 4 |
| Details | binding site for residue K D 303 |
| Chain | Residue |
| A | ALA143 |
| A | EDO307 |
| A | HOH486 |
| D | ASP142 |
| site_id | AD7 |
| Number of Residues | 3 |
| Details | binding site for residue EDO D 304 |
| Chain | Residue |
| D | VAL84 |
| D | VAL127 |
| D | ARG134 |
| site_id | AD8 |
| Number of Residues | 2 |
| Details | binding site for residue EDO D 305 |
| Chain | Residue |
| D | PRO190 |
| D | HOH431 |
| site_id | AD9 |
| Number of Residues | 8 |
| Details | binding site for residue EDO D 306 |
| Chain | Residue |
| D | ARG47 |
| D | PRO48 |
| D | VAL49 |
| D | ASP198 |
| D | GLU199 |
| D | LEU201 |
| D | LEU202 |
| D | HOH406 |
| site_id | AE1 |
| Number of Residues | 4 |
| Details | binding site for residue EDO D 307 |
| Chain | Residue |
| A | PHE65 |
| A | GLU69 |
| A | ILE191 |
| D | GLN76 |
| site_id | AE2 |
| Number of Residues | 1 |
| Details | binding site for residue BR F 101 |
| Chain | Residue |
| F | GLU16 |
| site_id | AE3 |
| Number of Residues | 7 |
| Details | binding site for residue EDO F 102 |
| Chain | Residue |
| F | ILE44 |
| F | PHE45 |
| F | ALA46 |
| F | GLY47 |
| F | THR66 |
| F | HIS68 |
| F | HOH205 |
| site_id | AE4 |
| Number of Residues | 6 |
| Details | binding site for residue EDO F 103 |
| Chain | Residue |
| A | GLY116 |
| F | LYS6 |
| F | THR66 |
| F | HIS68 |
| F | HOH209 |
| F | HOH213 |
| site_id | AE5 |
| Number of Residues | 10 |
| Details | binding site for Di-peptide NLE E 1 and GLN E 2 |
| Chain | Residue |
| E | LYS63 |
| E | GLU64 |
| A | GLU164 |
| B | PRO37 |
| B | ASP39 |
| E | ILE3 |
| E | THR14 |
| E | LEU15 |
| E | GLU16 |
| E | VAL17 |
| site_id | AE6 |
| Number of Residues | 33 |
| Details | binding site for Di-peptide LYS E 27 and GLY F 76 |
| Chain | Residue |
| D | GLN89 |
| D | ASN93 |
| D | CYS95 |
| D | VAL166 |
| D | LEU168 |
| D | HIS169 |
| E | ILE23 |
| E | GLU24 |
| E | ASN25 |
| E | VAL26 |
| E | ALA28 |
| E | LYS29 |
| E | ILE30 |
| E | GLN31 |
| E | GLN41 |
| E | ARG42 |
| E | LEU43 |
| E | LEU50 |
| E | ASP52 |
| E | GLY75 |
| F | ILE23 |
| F | GLU24 |
| F | ASN25 |
| F | VAL26 |
| F | ALA28 |
| F | LYS29 |
| F | ILE30 |
| F | GLN31 |
| F | GLN41 |
| F | ASP52 |
| F | GLY75 |
| F | HOH201 |
| F | HOH212 |
| site_id | AE7 |
| Number of Residues | 24 |
| Details | binding site for Di-peptide GLY E 76 and CYS D 95 |
| Chain | Residue |
| A | GLN78 |
| A | ASP79 |
| A | ASN192 |
| A | HIS193 |
| A | GLY194 |
| D | LYS72 |
| D | ILE73 |
| D | LYS74 |
| D | SER75 |
| D | GLY77 |
| D | GLN89 |
| D | ASN93 |
| D | ALA94 |
| D | GLY96 |
| D | THR97 |
| D | ILE98 |
| D | GLY99 |
| D | VAL166 |
| D | LEU168 |
| D | HIS169 |
| D | PHE170 |
| D | EDO307 |
| D | HOH442 |
| E | GLY75 |
Functional Information from PROSITE/UniProt
| site_id | PS00299 |
| Number of Residues | 26 |
| Details | UBIQUITIN_1 Ubiquitin domain signature. KakIqDkegIPpdqQrLIFaGkqleD |
| Chain | Residue | Details |
| B | LYS27-ASP52 | |
| C | LYS27-ASP52 |
| site_id | PS00140 |
| Number of Residues | 17 |
| Details | UCH_1 Ubiquitin carboxyl-terminal hydrolase family 1 cysteine active-site. QtisNACGtigLIHAIA |
| Chain | Residue | Details |
| A | GLN89-ALA105 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 4 |
| Details | SITE: Interacts with activating enzyme |
| Chain | Residue | Details |
| F | ARG54 | |
| F | ARG72 | |
| C | ARG54 | |
| C | ARG72 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 2 |
| Details | SITE: Essential for function |
| Chain | Residue | Details |
| C | HIS68 | |
| F | HIS68 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine; by PINK1 => ECO:0000269|PubMed:24660806, ECO:0000269|PubMed:24751536, ECO:0000269|PubMed:24784582, ECO:0000269|PubMed:25527291 |
| Chain | Residue | Details |
| C | SER65 | |
| F | SER65 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 2 |
| Details | MOD_RES: (Microbial infection) ADP-ribosylthreonine => ECO:0000269|PubMed:32330457 |
| Chain | Residue | Details |
| C | THR66 | |
| F | THR66 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 2 |
| Details | MOD_RES: ADP-ribosylglycine => ECO:0000269|PubMed:28525742 |
| Chain | Residue | Details |
| C | GLY76 | |
| F | GLY76 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 2 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16443603 |
| Chain | Residue | Details |
| C | LYS6 | |
| F | LYS6 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 4 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins) |
| Chain | Residue | Details |
| C | GLY76 | |
| F | GLY76 |
| site_id | SWS_FT_FI8 |
| Number of Residues | 4 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16443603, ECO:0000269|PubMed:16543144 |
| Chain | Residue | Details |
| F | LYS11 | |
| F | LYS48 | |
| C | LYS11 | |
| C | LYS48 |
| site_id | SWS_FT_FI9 |
| Number of Residues | 2 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000305|PubMed:15466860 |
| Chain | Residue | Details |
| C | LYS27 | |
| F | LYS27 |
| site_id | SWS_FT_FI10 |
| Number of Residues | 2 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16543144, ECO:0000269|PubMed:25752573, ECO:0000269|PubMed:25752577, ECO:0000269|PubMed:34239127 |
| Chain | Residue | Details |
| C | LYS29 | |
| F | LYS29 |
| site_id | SWS_FT_FI11 |
| Number of Residues | 2 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:25752577 |
| Chain | Residue | Details |
| C | LYS33 | |
| F | LYS33 |
| site_id | SWS_FT_FI12 |
| Number of Residues | 2 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16543144, ECO:0000269|PubMed:18719106 |
| Chain | Residue | Details |
| C | LYS63 | |
| F | LYS63 |
Catalytic Information from CSA
| site_id | MCSA1 |
| Number of Residues | 4 |
| Details | M-CSA 597 |
| Chain | Residue | Details |
| A | CYS95 | covalent catalysis, proton shuttle (general acid/base) |
| A | GLN89 | electrostatic stabiliser |
| A | HIS169 | proton shuttle (general acid/base) |
| A | ASP184 | electrostatic stabiliser |
| site_id | MCSA2 |
| Number of Residues | 4 |
| Details | M-CSA 597 |
| Chain | Residue | Details |
| D | CYS95 | covalent catalysis, proton shuttle (general acid/base) |
| D | GLN89 | electrostatic stabiliser |
| D | HIS169 | proton shuttle (general acid/base) |
| D | ASP184 | electrostatic stabiliser |
