3NS8
Crystal structure of an open conformation of Lys48-linked diubiquitin at pH 7.5
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE GOL A 77 |
| Chain | Residue |
| A | GLU51 |
| A | ASP52 |
| A | ARG72 |
| A | HOH81 |
| A | HOH102 |
| A | HOH111 |
| B | GLY47 |
| B | LYS48 |
| B | GLN49 |
| site_id | AC2 |
| Number of Residues | 11 |
| Details | BINDING SITE FOR RESIDUE GOL B 77 |
| Chain | Residue |
| A | LYS48 |
| A | GLN49 |
| A | HOH90 |
| A | HOH130 |
| B | LYS27 |
| B | GLN49 |
| B | LEU50 |
| B | GLU51 |
| B | ASP52 |
| B | ARG72 |
| B | HOH96 |
| site_id | AC3 |
| Number of Residues | 11 |
| Details | BINDING SITE FOR RESIDUE EPE B 78 |
| Chain | Residue |
| B | ASN25 |
| B | ALA28 |
| B | LYS29 |
| B | ASP32 |
| B | PHE45 |
| B | SER65 |
| B | THR66 |
| B | HIS68 |
| B | HOH87 |
| B | HOH95 |
| B | HOH124 |
Functional Information from PROSITE/UniProt
| site_id | PS00299 |
| Number of Residues | 26 |
| Details | UBIQUITIN_1 Ubiquitin domain signature. KakIqDkegIPpdqQrLIFaGkqleD |
| Chain | Residue | Details |
| A | LYS27-ASP52 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 4 |
| Details | SITE: Interacts with activating enzyme |
| Chain | Residue | Details |
| A | ARG54 | |
| A | ARG72 | |
| B | ARG54 | |
| B | ARG72 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 2 |
| Details | SITE: Essential for function |
| Chain | Residue | Details |
| A | HIS68 | |
| B | 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 |
| A | SER65 | |
| B | SER65 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 2 |
| Details | MOD_RES: (Microbial infection) ADP-ribosylthreonine => ECO:0000269|PubMed:32330457 |
| Chain | Residue | Details |
| A | THR66 | |
| B | THR66 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 2 |
| Details | MOD_RES: ADP-ribosylglycine => ECO:0000269|PubMed:28525742 |
| Chain | Residue | Details |
| A | GLY76 | |
| B | 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 |
| A | LYS6 | |
| B | 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 |
| A | GLY76 | |
| B | 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 |
| A | LYS11 | |
| A | LYS48 | |
| B | LYS11 | |
| B | 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 |
| A | LYS27 | |
| B | 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 |
| A | LYS29 | |
| B | 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 |
| A | LYS33 | |
| B | 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 |
| A | LYS63 | |
| B | LYS63 |
