5F0L
Structure of retromer VPS26-VPS35 subunits bound to SNX3 and DMT1
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0015031 | biological_process | protein transport |
| A | 0030906 | cellular_component | retromer, cargo-selective complex |
| A | 0042147 | biological_process | retrograde transport, endosome to Golgi |
| B | 0005515 | molecular_function | protein binding |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0005764 | cellular_component | lysosome |
| B | 0005768 | cellular_component | endosome |
| B | 0005769 | cellular_component | early endosome |
| B | 0005829 | cellular_component | cytosol |
| B | 0006886 | biological_process | intracellular protein transport |
| B | 0010008 | cellular_component | endosome membrane |
| B | 0015031 | biological_process | protein transport |
| B | 0016241 | biological_process | regulation of macroautophagy |
| B | 0030904 | cellular_component | retromer complex |
| B | 0030906 | cellular_component | retromer, cargo-selective complex |
| B | 0031982 | cellular_component | vesicle |
| B | 0032456 | biological_process | endocytic recycling |
| B | 0042147 | biological_process | retrograde transport, endosome to Golgi |
| B | 0097422 | cellular_component | tubular endosome |
| C | 0005515 | molecular_function | protein binding |
| C | 0005737 | cellular_component | cytoplasm |
| C | 0005769 | cellular_component | early endosome |
| C | 0005829 | cellular_component | cytosol |
| C | 0008289 | molecular_function | lipid binding |
| C | 0009617 | biological_process | response to bacterium |
| C | 0010008 | cellular_component | endosome membrane |
| C | 0010314 | molecular_function | phosphatidylinositol-5-phosphate binding |
| C | 0010324 | biological_process | membrane invagination |
| C | 0010976 | biological_process | positive regulation of neuron projection development |
| C | 0015031 | biological_process | protein transport |
| C | 0019903 | molecular_function | protein phosphatase binding |
| C | 0022615 | biological_process | protein to membrane docking |
| C | 0030111 | biological_process | regulation of Wnt signaling pathway |
| C | 0030136 | cellular_component | clathrin-coated vesicle |
| C | 0030904 | cellular_component | retromer complex |
| C | 0031410 | cellular_component | cytoplasmic vesicle |
| C | 0031901 | cellular_component | early endosome membrane |
| C | 0032009 | cellular_component | early phagosome |
| C | 0032266 | molecular_function | phosphatidylinositol-3-phosphate binding |
| C | 0032456 | biological_process | endocytic recycling |
| C | 0034499 | biological_process | late endosome to Golgi transport |
| C | 0035091 | molecular_function | phosphatidylinositol binding |
| C | 0042177 | biological_process | negative regulation of protein catabolic process |
| C | 0045335 | cellular_component | phagocytic vesicle |
| C | 0046597 | biological_process | host-mediated suppression of symbiont invasion |
| C | 0050765 | biological_process | negative regulation of phagocytosis |
| C | 0051224 | biological_process | negative regulation of protein transport |
| C | 0070062 | cellular_component | extracellular exosome |
| C | 0070273 | molecular_function | phosphatidylinositol-4-phosphate binding |
| C | 0070676 | biological_process | intralumenal vesicle formation |
| C | 0080025 | molecular_function | phosphatidylinositol-3,5-bisphosphate binding |
| C | 1901981 | molecular_function | phosphatidylinositol phosphate binding |
| C | 1905394 | molecular_function | retromer complex binding |
| C | 2000642 | biological_process | negative regulation of early endosome to late endosome transport |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 2 |
| Details | binding site for residue SO4 A 501 |
| Chain | Residue |
| A | ALA101 |
| A | GLY102 |
| site_id | AC2 |
| Number of Residues | 5 |
| Details | binding site for residue SO4 A 502 |
| Chain | Residue |
| A | LEU43 |
| A | LYS44 |
| A | SER47 |
| A | LEU97 |
| A | ALA101 |
| site_id | AC3 |
| Number of Residues | 7 |
| Details | binding site for residue SO4 A 503 |
| Chain | Residue |
| A | THR278 |
| A | LEU279 |
| A | ASN280 |
| A | ILE327 |
| C | ASP107 |
| A | LEU276 |
| A | GLN277 |
| site_id | AC4 |
| Number of Residues | 4 |
| Details | binding site for residue GOL A 504 |
| Chain | Residue |
| A | LYS38 |
| A | LEU39 |
| A | MET40 |
| A | ASP41 |
| site_id | AC5 |
| Number of Residues | 2 |
| Details | binding site for residue GOL A 505 |
| Chain | Residue |
| A | LYS120 |
| A | ASN159 |
| site_id | AC6 |
| Number of Residues | 2 |
| Details | binding site for residue EDO A 506 |
| Chain | Residue |
| A | LYS296 |
| A | ASP346 |
| site_id | AC7 |
| Number of Residues | 3 |
| Details | binding site for residue EDO A 507 |
| Chain | Residue |
| A | ARG254 |
| A | GLU288 |
| A | HIS290 |
| site_id | AC8 |
| Number of Residues | 2 |
| Details | binding site for residue EDO A 508 |
| Chain | Residue |
| A | SER353 |
| A | ASN356 |
| site_id | AC9 |
| Number of Residues | 1 |
| Details | binding site for residue EDO A 509 |
| Chain | Residue |
| A | ARG365 |
| site_id | AD1 |
| Number of Residues | 5 |
| Details | binding site for residue EDO A 510 |
| Chain | Residue |
| A | ALA188 |
| A | GLN249 |
| C | GLN16 |
| C | LEU18 |
| C | ALA21 |
| site_id | AD2 |
| Number of Residues | 2 |
| Details | binding site for residue EDO A 511 |
| Chain | Residue |
| A | ARG204 |
| C | ARG52 |
| site_id | AD3 |
| Number of Residues | 4 |
| Details | binding site for residue SO4 B 401 |
| Chain | Residue |
| A | GLY102 |
| A | ASN103 |
| B | GLU208 |
| B | LYS232 |
| site_id | AD4 |
| Number of Residues | 4 |
| Details | binding site for residue SO4 B 402 |
| Chain | Residue |
| B | TYR118 |
| B | ASP263 |
| B | VAL264 |
| B | ASN265 |
| site_id | AD5 |
| Number of Residues | 5 |
| Details | binding site for residue SO4 B 403 |
| Chain | Residue |
| B | PRO158 |
| B | ASP159 |
| B | VAL160 |
| B | LYS184 |
| B | EDO408 |
| site_id | AD6 |
| Number of Residues | 4 |
| Details | binding site for residue SO4 B 404 |
| Chain | Residue |
| B | GLN210 |
| B | LYS232 |
| B | ARG285 |
| D | LEU554 |
| site_id | AD7 |
| Number of Residues | 6 |
| Details | binding site for residue GOL B 405 |
| Chain | Residue |
| B | ASP81 |
| B | ASN84 |
| B | TYR157 |
| B | LYS182 |
| B | HIS186 |
| C | ARG9 |
| site_id | AD8 |
| Number of Residues | 3 |
| Details | binding site for residue GOL B 406 |
| Chain | Residue |
| B | HIS39 |
| B | TYR40 |
| B | ASP148 |
| site_id | AD9 |
| Number of Residues | 4 |
| Details | binding site for residue EDO B 407 |
| Chain | Residue |
| A | ARG54 |
| B | GLN205 |
| B | GLU234 |
| B | ASP237 |
| site_id | AE1 |
| Number of Residues | 3 |
| Details | binding site for residue EDO B 408 |
| Chain | Residue |
| B | THR156 |
| B | ILE293 |
| B | SO4403 |
| site_id | AE2 |
| Number of Residues | 2 |
| Details | binding site for residue EDO B 409 |
| Chain | Residue |
| B | ARG69 |
| B | GLU94 |
| site_id | AE3 |
| Number of Residues | 3 |
| Details | binding site for residue EDO B 410 |
| Chain | Residue |
| B | ALA124 |
| B | LYS213 |
| B | GLU228 |
| site_id | AE4 |
| Number of Residues | 4 |
| Details | binding site for residue EDO B 411 |
| Chain | Residue |
| B | GLU77 |
| B | ASN80 |
| B | ALA124 |
| B | ARG127 |
| site_id | AE5 |
| Number of Residues | 5 |
| Details | binding site for residue EDO B 412 |
| Chain | Residue |
| B | ILE216 |
| B | GLY218 |
| B | ASP263 |
| B | LYS267 |
| B | SER269 |
| site_id | AE6 |
| Number of Residues | 4 |
| Details | binding site for residue EDO B 413 |
| Chain | Residue |
| B | GLN153 |
| B | ALA155 |
| B | PRO259 |
| B | ARG296 |
| site_id | AE7 |
| Number of Residues | 3 |
| Details | binding site for residue EDO B 414 |
| Chain | Residue |
| B | ASN80 |
| B | LYS82 |
| B | ASN162 |
| site_id | AE8 |
| Number of Residues | 1 |
| Details | binding site for residue EDO B 415 |
| Chain | Residue |
| B | ARG139 |
| site_id | AE9 |
| Number of Residues | 3 |
| Details | binding site for residue EDO B 416 |
| Chain | Residue |
| B | GLU177 |
| B | LYS194 |
| C | LYS14 |
| site_id | AF1 |
| Number of Residues | 6 |
| Details | binding site for residue SO4 C 201 |
| Chain | Residue |
| C | PHE46 |
| C | ARG70 |
| C | TYR71 |
| C | SER72 |
| C | ARG118 |
| C | SO4202 |
| site_id | AF2 |
| Number of Residues | 6 |
| Details | binding site for residue SO4 C 202 |
| Chain | Residue |
| C | LYS95 |
| C | ALA96 |
| C | GLN100 |
| C | ILE109 |
| C | ARG118 |
| C | SO4201 |
| site_id | AF3 |
| Number of Residues | 4 |
| Details | binding site for residue SO4 C 203 |
| Chain | Residue |
| C | SER34 |
| C | ASN35 |
| C | PRO36 |
| C | LYS119 |
| site_id | AF4 |
| Number of Residues | 4 |
| Details | binding site for residue GOL C 204 |
| Chain | Residue |
| B | LEU199 |
| B | ARG201 |
| B | LYS242 |
| C | SER26 |
| site_id | AF5 |
| Number of Residues | 1 |
| Details | binding site for residue GOL C 205 |
| Chain | Residue |
| C | LYS63 |
| site_id | AF6 |
| Number of Residues | 4 |
| Details | binding site for residue EDO C 206 |
| Chain | Residue |
| C | ARG99 |
| C | GLN100 |
| C | LEU101 |
| C | ASP106 |
| site_id | AF7 |
| Number of Residues | 4 |
| Details | binding site for residue EDO C 207 |
| Chain | Residue |
| C | THR48 |
| C | ARG68 |
| C | ASP73 |
| C | ILE149 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 29 |
| Details | Region: {"description":"Interaction with SNX3","evidences":[{"source":"PubMed","id":"24344282","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 124 |
| Details | Domain: {"description":"PX","evidences":[{"source":"PROSITE-ProRule","id":"PRU00147","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 4 |
| Details | Binding site: {"evidences":[{"evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI4 |
| Number of Residues | 1 |
| Details | Modified residue: {"description":"Omega-N-methylarginine","evidences":[{"source":"PubMed","id":"24129315","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI5 |
| Number of Residues | 1 |
| Details | Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"18669648","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"20068231","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI6 |
| Number of Residues | 2 |
| Details | Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)","evidences":[{"source":"PubMed","id":"28112733","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI7 |
| Number of Residues | 4 |
| Details | Region: {"description":"Required for early endosome targeting","evidences":[{"source":"PubMed","id":"12475959","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
