4XKL
Crystal structure of NDP52 ZF2 in complex with mono-ubiquitin
Functional Information from PDB Data
site_id | AC1 |
Number of Residues | 9 |
Details | binding site for residue GOL A 101 |
Chain | Residue |
A | THR7 |
A | LEU8 |
A | THR9 |
A | LEU69 |
A | VAL70 |
A | LEU71 |
A | HOH213 |
C | LEU71 |
D | HOH601 |
site_id | AC2 |
Number of Residues | 4 |
Details | binding site for residue ACT B 502 |
Chain | Residue |
B | ASP426 |
B | LYS427 |
B | ILE428 |
B | HOH615 |
site_id | AC3 |
Number of Residues | 4 |
Details | binding site for residue ZN B 503 |
Chain | Residue |
B | CYS422 |
B | CYS425 |
B | HIS440 |
B | HIS444 |
site_id | AC4 |
Number of Residues | 8 |
Details | binding site for residue GOL C 101 |
Chain | Residue |
C | THR7 |
C | LEU8 |
C | THR9 |
C | LEU69 |
C | VAL70 |
C | LEU71 |
C | HOH207 |
C | HOH208 |
site_id | AC5 |
Number of Residues | 2 |
Details | binding site for residue ACT C 102 |
Chain | Residue |
C | LYS11 |
C | THR12 |
site_id | AC6 |
Number of Residues | 1 |
Details | binding site for residue ACT D 501 |
Chain | Residue |
D | CYS419 |
site_id | AC7 |
Number of Residues | 4 |
Details | binding site for residue ZN D 502 |
Chain | Residue |
D | CYS422 |
D | CYS425 |
D | HIS440 |
D | HIS444 |
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 | 150 |
Details | Domain: {"description":"Ubiquitin-like","evidences":[{"source":"PROSITE-ProRule","id":"PRU00214","evidenceCode":"ECO:0000255"}]} |
Chain | Residue | Details |
site_id | SWS_FT_FI2 |
Number of Residues | 4 |
Details | Site: {"description":"Interacts with activating enzyme"} |
Chain | Residue | Details |
site_id | SWS_FT_FI3 |
Number of Residues | 2 |
Details | Site: {"description":"Essential for function"} |
Chain | Residue | Details |
site_id | SWS_FT_FI4 |
Number of Residues | 2 |
Details | Modified residue: {"description":"Phosphoserine; by PINK1","evidences":[{"source":"PubMed","id":"24660806","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"24751536","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"24784582","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"25474007","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"25527291","evidenceCode":"ECO:0000269"}]} |
Chain | Residue | Details |
site_id | SWS_FT_FI5 |
Number of Residues | 2 |
Details | Modified residue: {"description":"(Microbial infection) ADP-ribosylthreonine","evidences":[{"source":"PubMed","id":"32330457","evidenceCode":"ECO:0000269"}]} |
Chain | Residue | Details |
site_id | SWS_FT_FI6 |
Number of Residues | 2 |
Details | Modified residue: {"description":"ADP-ribosylglycine","evidences":[{"source":"PubMed","id":"28525742","evidenceCode":"ECO:0000269"}]} |
Chain | Residue | Details |
site_id | SWS_FT_FI7 |
Number of Residues | 2 |
Details | Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"16443603","evidenceCode":"ECO:0000269"}]} |
Chain | Residue | Details |
site_id | SWS_FT_FI8 |
Number of Residues | 4 |
Details | Cross-link: {"description":"Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)"} |
Chain | Residue | Details |
site_id | SWS_FT_FI9 |
Number of Residues | 4 |
Details | Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"16443603","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16543144","evidenceCode":"ECO:0000269"}]} |
Chain | Residue | Details |
site_id | SWS_FT_FI10 |
Number of Residues | 2 |
Details | Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"15466860","evidenceCode":"ECO:0000305"}]} |
Chain | Residue | Details |
site_id | SWS_FT_FI11 |
Number of Residues | 2 |
Details | Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"16543144","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"25752573","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"25752577","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"34239127","evidenceCode":"ECO:0000269"}]} |
Chain | Residue | Details |
site_id | SWS_FT_FI12 |
Number of Residues | 2 |
Details | Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"25752577","evidenceCode":"ECO:0000269"}]} |
Chain | Residue | Details |
site_id | SWS_FT_FI13 |
Number of Residues | 2 |
Details | Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"16543144","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"18719106","evidenceCode":"ECO:0000269"}]} |
Chain | Residue | Details |
site_id | SWS_FT_FI14 |
Number of Residues | 50 |
Details | Zinc finger: {"description":"UBZ1-type","evidences":[{"source":"PROSITE-ProRule","id":"PRU01253","evidenceCode":"ECO:0000255"}]} |
Chain | Residue | Details |
site_id | SWS_FT_FI15 |
Number of Residues | 8 |
Details | Binding site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU01253","evidenceCode":"ECO:0000255"}]} |
Chain | Residue | Details |
site_id | SWS_FT_FI16 |
Number of Residues | 2 |
Details | Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]} |
Chain | Residue | Details |