4U1M
HLA class I micropolymorphisms determine peptide-HLA landscape and dictate differential HIV-1 escape through identical epitopes
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| B | 0000139 | cellular_component | Golgi membrane |
| B | 0002376 | biological_process | immune system process |
| B | 0002474 | biological_process | antigen processing and presentation of peptide antigen via MHC class I |
| B | 0002477 | biological_process | antigen processing and presentation of exogenous peptide antigen via MHC class Ib |
| B | 0002502 | biological_process | peptide antigen assembly with MHC class I protein complex |
| B | 0002503 | biological_process | peptide antigen assembly with MHC class II protein complex |
| B | 0002715 | biological_process | regulation of natural killer cell mediated immunity |
| B | 0002726 | biological_process | positive regulation of T cell cytokine production |
| B | 0005198 | molecular_function | structural molecule activity |
| B | 0005515 | molecular_function | protein binding |
| B | 0005576 | cellular_component | extracellular region |
| B | 0005615 | cellular_component | extracellular space |
| B | 0005765 | cellular_component | lysosomal membrane |
| B | 0005783 | cellular_component | endoplasmic reticulum |
| B | 0005788 | cellular_component | endoplasmic reticulum lumen |
| B | 0005794 | cellular_component | Golgi apparatus |
| B | 0005886 | cellular_component | plasma membrane |
| B | 0005925 | cellular_component | focal adhesion |
| B | 0006879 | biological_process | intracellular iron ion homeostasis |
| B | 0006955 | biological_process | immune response |
| B | 0007608 | biological_process | sensory perception of smell |
| B | 0007611 | biological_process | learning or memory |
| B | 0009897 | cellular_component | external side of plasma membrane |
| B | 0009986 | cellular_component | cell surface |
| B | 0010038 | biological_process | response to metal ion |
| B | 0012507 | cellular_component | ER to Golgi transport vesicle membrane |
| B | 0016020 | cellular_component | membrane |
| B | 0019885 | biological_process | antigen processing and presentation of endogenous peptide antigen via MHC class I |
| B | 0019886 | biological_process | antigen processing and presentation of exogenous peptide antigen via MHC class II |
| B | 0023026 | molecular_function | MHC class II protein complex binding |
| B | 0030670 | cellular_component | phagocytic vesicle membrane |
| B | 0031901 | cellular_component | early endosome membrane |
| B | 0031902 | cellular_component | late endosome membrane |
| B | 0031905 | cellular_component | early endosome lumen |
| B | 0032398 | cellular_component | MHC class Ib protein complex |
| B | 0033572 | biological_process | transferrin transport |
| B | 0034756 | biological_process | regulation of iron ion transport |
| B | 0034757 | biological_process | negative regulation of iron ion transport |
| B | 0035580 | cellular_component | specific granule lumen |
| B | 0042605 | molecular_function | peptide antigen binding |
| B | 0042612 | cellular_component | MHC class I protein complex |
| B | 0042613 | cellular_component | MHC class II protein complex |
| B | 0042802 | molecular_function | identical protein binding |
| B | 0042803 | molecular_function | protein homodimerization activity |
| B | 0042824 | cellular_component | MHC class I peptide loading complex |
| B | 0048260 | biological_process | positive regulation of receptor-mediated endocytosis |
| B | 0048261 | biological_process | negative regulation of receptor-mediated endocytosis |
| B | 0050680 | biological_process | negative regulation of epithelial cell proliferation |
| B | 0050768 | biological_process | negative regulation of neurogenesis |
| B | 0050778 | biological_process | positive regulation of immune response |
| B | 0050870 | biological_process | positive regulation of T cell activation |
| B | 0051289 | biological_process | protein homotetramerization |
| B | 0055038 | cellular_component | recycling endosome membrane |
| B | 0070062 | cellular_component | extracellular exosome |
| B | 0071281 | biological_process | cellular response to iron ion |
| B | 0071316 | biological_process | cellular response to nicotine |
| B | 1904724 | cellular_component | tertiary granule lumen |
| B | 1990000 | biological_process | amyloid fibril formation |
| B | 1990712 | cellular_component | HFE-transferrin receptor complex |
| B | 2000774 | biological_process | positive regulation of cellular senescence |
| B | 2000978 | biological_process | negative regulation of forebrain neuron differentiation |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 8 |
| Details | binding site for residue EDO A 301 |
| Chain | Residue |
| A | ASP122 |
| A | TYR123 |
| A | ALA125 |
| A | THR134 |
| A | ALA136 |
| A | HOH533 |
| A | HOH671 |
| A | HOH432 |
| site_id | AC2 |
| Number of Residues | 5 |
| Details | binding site for residue EDO A 302 |
| Chain | Residue |
| A | GLU46 |
| A | PRO47 |
| A | ARG48 |
| A | HOH504 |
| A | ARG35 |
| site_id | AC3 |
| Number of Residues | 7 |
| Details | binding site for residue EDO A 303 |
| Chain | Residue |
| A | SER38 |
| A | SER195 |
| A | ASP196 |
| A | EDO314 |
| A | HOH401 |
| A | HOH478 |
| A | HOH498 |
| site_id | AC4 |
| Number of Residues | 5 |
| Details | binding site for residue EDO A 304 |
| Chain | Residue |
| A | GLU166 |
| A | TRP167 |
| A | ARG170 |
| A | EDO305 |
| A | HOH681 |
| site_id | AC5 |
| Number of Residues | 5 |
| Details | binding site for residue EDO A 305 |
| Chain | Residue |
| A | THR163 |
| A | GLU166 |
| A | TRP167 |
| A | EDO304 |
| A | HOH506 |
| site_id | AC6 |
| Number of Residues | 6 |
| Details | binding site for residue EDO A 306 |
| Chain | Residue |
| A | ASP227 |
| A | GLU229 |
| A | ALA246 |
| A | VAL247 |
| A | HOH442 |
| A | HOH443 |
| site_id | AC7 |
| Number of Residues | 5 |
| Details | binding site for residue EDO A 307 |
| Chain | Residue |
| A | GLU58 |
| A | TYR59 |
| A | ARG62 |
| A | HOH426 |
| C | ARG1 |
| site_id | AC8 |
| Number of Residues | 7 |
| Details | binding site for residue EDO A 308 |
| Chain | Residue |
| A | TYR85 |
| A | TYR118 |
| A | LYS121 |
| A | ASP122 |
| A | ASP137 |
| A | HOH445 |
| A | HOH422 |
| site_id | AC9 |
| Number of Residues | 6 |
| Details | binding site for residue EDO A 309 |
| Chain | Residue |
| A | GLU148 |
| A | ARG151 |
| A | GLU154 |
| A | HOH544 |
| A | HOH586 |
| A | HOH603 |
| site_id | AD1 |
| Number of Residues | 8 |
| Details | binding site for residue EDO A 310 |
| Chain | Residue |
| A | GLY207 |
| A | ALA236 |
| A | ASP238 |
| A | THR240 |
| A | PHE241 |
| A | GLN242 |
| A | HOH472 |
| B | ARG12 |
| site_id | AD2 |
| Number of Residues | 5 |
| Details | binding site for residue EDO A 311 |
| Chain | Residue |
| A | THR73 |
| A | HOH635 |
| A | HOH403 |
| C | PRO5 |
| C | LEU6 |
| site_id | AD3 |
| Number of Residues | 6 |
| Details | binding site for residue EDO A 312 |
| Chain | Residue |
| A | ALA149 |
| A | ARG151 |
| B | ASP38 |
| B | ARG45 |
| B | ARG81 |
| B | GOL309 |
| site_id | AD4 |
| Number of Residues | 6 |
| Details | binding site for residue EDO A 313 |
| Chain | Residue |
| A | ALA135 |
| A | ASP137 |
| A | GLN141 |
| A | GLN144 |
| A | HOH409 |
| A | HOH555 |
| site_id | AD5 |
| Number of Residues | 8 |
| Details | binding site for residue EDO A 314 |
| Chain | Residue |
| A | LYS68 |
| A | GLN72 |
| A | ILE194 |
| A | SER195 |
| A | EDO303 |
| A | HOH401 |
| A | HOH609 |
| A | HOH512 |
| site_id | AD6 |
| Number of Residues | 7 |
| Details | binding site for residue EDO A 315 |
| Chain | Residue |
| A | GLN70 |
| A | THR73 |
| A | ASP74 |
| A | SER77 |
| A | GOL319 |
| C | ARG7 |
| C | HOH205 |
| site_id | AD7 |
| Number of Residues | 6 |
| Details | binding site for residue EDO A 316 |
| Chain | Residue |
| A | HOH576 |
| A | HIS188 |
| A | VAL189 |
| A | LEU272 |
| A | ARG273 |
| A | GLU275 |
| site_id | AD8 |
| Number of Residues | 6 |
| Details | binding site for residue EDO A 317 |
| Chain | Residue |
| A | ARG21 |
| A | ARG131 |
| A | HOH411 |
| B | HIS51 |
| B | HOH469 |
| B | HOH435 |
| site_id | AD9 |
| Number of Residues | 12 |
| Details | binding site for residue GOL A 318 |
| Chain | Residue |
| A | HIS3 |
| A | ASP29 |
| A | LEU179 |
| A | GLU180 |
| A | ARG181 |
| A | ALA182 |
| A | PRO210 |
| A | GLU264 |
| A | HOH430 |
| A | HOH446 |
| A | HOH551 |
| A | HOH493 |
| site_id | AE1 |
| Number of Residues | 9 |
| Details | binding site for residue GOL A 319 |
| Chain | Residue |
| A | ASN114 |
| A | TYR116 |
| A | TRP147 |
| A | VAL152 |
| A | ASP156 |
| A | EDO315 |
| C | LEU6 |
| C | ARG7 |
| C | EDO101 |
| site_id | AE2 |
| Number of Residues | 10 |
| Details | binding site for residue EDO B 301 |
| Chain | Residue |
| A | LEU206 |
| A | ARG234 |
| A | GLN242 |
| B | TYR10 |
| B | SER11 |
| B | HIS13 |
| B | PRO14 |
| B | HOH441 |
| B | HOH474 |
| B | HOH447 |
| site_id | AE3 |
| Number of Residues | 3 |
| Details | binding site for residue EDO B 302 |
| Chain | Residue |
| B | LYS94 |
| B | TRP95 |
| B | HOH427 |
| site_id | AE4 |
| Number of Residues | 6 |
| Details | binding site for residue EDO B 303 |
| Chain | Residue |
| A | ARG151 |
| B | GLU36 |
| B | ASP38 |
| B | ARG81 |
| B | ASN83 |
| B | PRO90 |
| site_id | AE5 |
| Number of Residues | 8 |
| Details | binding site for residue EDO B 304 |
| Chain | Residue |
| A | TYR27 |
| A | PRO235 |
| B | SER52 |
| B | TYR63 |
| B | LEU65 |
| B | HOH428 |
| B | HOH419 |
| B | HOH502 |
| site_id | AE6 |
| Number of Residues | 4 |
| Details | binding site for residue EDO B 305 |
| Chain | Residue |
| B | ASN17 |
| B | GLY18 |
| B | THR73 |
| B | GLU74 |
| site_id | AE7 |
| Number of Residues | 4 |
| Details | binding site for residue EDO B 306 |
| Chain | Residue |
| A | ASP37 |
| B | ASP53 |
| B | LEU54 |
| B | HOH435 |
| site_id | AE8 |
| Number of Residues | 6 |
| Details | binding site for residue EDO B 307 |
| Chain | Residue |
| B | GLN8 |
| B | VAL9 |
| B | LYS94 |
| B | ASP96 |
| B | HOH430 |
| B | HOH448 |
| site_id | AE9 |
| Number of Residues | 5 |
| Details | binding site for residue EDO B 308 |
| Chain | Residue |
| A | SER92 |
| A | ARG157 |
| B | ASP34 |
| B | HOH401 |
| B | HOH464 |
| site_id | AF1 |
| Number of Residues | 4 |
| Details | binding site for residue GOL B 309 |
| Chain | Residue |
| A | EDO312 |
| B | GLY43 |
| B | ARG45 |
| B | ARG81 |
| site_id | AF2 |
| Number of Residues | 8 |
| Details | binding site for residue GOL B 310 |
| Chain | Residue |
| A | SER88 |
| A | ARG108 |
| B | ARG12 |
| B | HIS13 |
| B | PHE22 |
| B | HOH406 |
| B | HOH418 |
| B | HOH429 |
| site_id | AF3 |
| Number of Residues | 7 |
| Details | binding site for residue EDO C 101 |
| Chain | Residue |
| A | GLN70 |
| A | GOL319 |
| C | GLN3 |
| C | VAL4 |
| C | PRO5 |
| C | LEU6 |
| C | HOH205 |
Functional Information from PROSITE/UniProt
| site_id | PS00290 |
| Number of Residues | 7 |
| Details | IG_MHC Immunoglobulins and major histocompatibility complex proteins signature. YACRVNH |
| Chain | Residue | Details |
| B | TYR78-HIS84 | |
| A | TYR257-HIS263 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 174 |
| Details | Domain: {"description":"Ig-like C1-type"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 89 |
| Details | Region: {"description":"Alpha-1","evidences":[{"evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 91 |
| Details | Region: {"description":"Alpha-2","evidences":[{"evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI4 |
| Number of Residues | 91 |
| Details | Region: {"description":"Alpha-3","evidences":[{"evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI5 |
| Number of Residues | 6 |
| Details | Motif: {"description":"Bw6 motif","evidences":[{"source":"PubMed","id":"25480565","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI6 |
| Number of Residues | 7 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"25808313","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI7 |
| Number of Residues | 1 |
| Details | Glycosylation: {"description":"N-linked (GlcNAc...) asparagine","evidences":[{"source":"PubMed","id":"19159218","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI8 |
| Number of Residues | 1 |
| Details | Modified residue: {"description":"Pyrrolidone carboxylic acid; in form pI 5.3","evidences":[{"source":"PubMed","id":"7554280","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI9 |
| Number of Residues | 1 |
| Details | Glycosylation: {"description":"N-linked (Glc) (glycation) isoleucine; in hemodialysis-associated amyloidosis","evidences":[{"source":"PubMed","id":"7918443","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI10 |
| Number of Residues | 6 |
| Details | Glycosylation: {"description":"N-linked (Glc) (glycation) lysine; in vitro","evidences":[{"source":"PubMed","id":"7918443","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI11 |
| Number of Residues | 3 |
| Details | Motif: {"description":"PxxP; stabilizes the interaction of NEF/MHC-I with host AP1M1; necessary for MHC-I internalization","evidences":[{"source":"HAMAP-Rule","id":"MF_04078","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
