0.013812 0.000000 0.001929 0.000000 0.020416 0.000000 0.000000 0.000000 0.012012 0.00000 0.00000 0.00000 Speir, J.A. Wilson, I.A. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 2 90.00 97.95 90.00 72.400 48.980 84.060 C3 H7 N O2 89.093 y ALANINE L-peptide linking C6 H15 N4 O2 1 175.209 y ARGININE L-peptide linking C4 H8 N2 O3 132.118 y ASPARAGINE L-peptide linking C4 H7 N O4 133.103 y ASPARTIC ACID L-peptide linking C3 H7 N O2 S 121.158 y CYSTEINE L-peptide linking C5 H10 N2 O3 146.144 y GLUTAMINE L-peptide linking C5 H9 N O4 147.129 y GLUTAMIC ACID L-peptide linking C2 H5 N O2 75.067 y GLYCINE peptide linking C6 H10 N3 O2 1 156.162 y HISTIDINE L-peptide linking C6 H13 N O2 131.173 y ISOLEUCINE L-peptide linking C6 H13 N O2 131.173 y LEUCINE L-peptide linking C6 H15 N2 O2 1 147.195 y LYSINE L-peptide linking C5 H11 N O2 S 149.211 y METHIONINE L-peptide linking C8 H15 N O6 221.208 2-acetamido-2-deoxy-beta-D-glucopyranose N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE D-saccharide, beta linking C8 H15 N O6 221.208 2-acetamido-2-deoxy-alpha-D-glucopyranose N-acetyl-alpha-D-glucosamine; 2-acetamido-2-deoxy-alpha-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE D-saccharide, alpha linking C9 H11 N O2 165.189 y PHENYLALANINE L-peptide linking C5 H9 N O2 115.130 y PROLINE L-peptide linking C3 H7 N O3 105.093 y SERINE L-peptide linking C4 H9 N O3 119.119 y THREONINE L-peptide linking C11 H12 N2 O2 204.225 y TRYPTOPHAN L-peptide linking C9 H11 N O3 181.189 y TYROSINE L-peptide linking C5 H11 N O2 117.146 y VALINE L-peptide linking US Immunity IUNIEH 2048 1074-7613 8 553 562 10.1016/S1074-7613(00)80560-9 9620676 Structural basis of 2C TCR allorecognition of H-2Ld peptide complexes. 1998 US Science SCIEAS 0038 0036-8075 279 1166 Structural Basis of Plasticity in T Cell Receptor Recognition of a Self Peptide-Mhc Antigen 1998 10.2210/pdb1ldp/pdb pdb_00001ldp NAG A 1 HAS WRONG CHIRALITY AT ATOM C1 NAG H 273 HAS WRONG CHIRALITY AT ATOM C1 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 298 1 DOUBLE-MIRROR FOCUSING CAMERAS AREA DETECTOR 1996-01 SIEMENS NI FILTER M x-ray 1 1.5418 1.0 1.5418 ROTATING ANODE ELLIOTT GX-18 ASPARAGINE LINKED N-ACETYL-GLUCOSAMINE CARBOHYDRATES AT CHAIN H, N86 AND N176 31388.924 MHC CLASS I H-2LD CHAIN H IS THE HEAVY CHAIN, PEPTIDE BINDING DOMAIN, CHAIN L IS THE LIGHT CHAIN OR BETA-2-MICROGLOBULIN HEAVY CHAIN TRUNCATED AFTER RESIDUE 274, B2M, LIGHT CHAIN TRUNCATED AFTER RESIDUE 99 1 man polymer ASPARAGINE LINKED N-ACETYL-GLUCOSAMINE CARBOHYDRATES AT CHAIN H, N86 AND N176 11704.359 MHC CLASS I H-2LD CHAIN H IS THE HEAVY CHAIN, PEPTIDE BINDING DOMAIN, CHAIN L IS THE LIGHT CHAIN OR BETA-2-MICROGLOBULIN HEAVY CHAIN TRUNCATED AFTER RESIDUE 274, B2M, LIGHT CHAIN TRUNCATED AFTER RESIDUE 99 1 man polymer 743.870 PEPTIDE CHAIN P IS A PEPTIDE, CHAIN Q IS A MODEL OF PEPTIDE QL9 DERIVED FROM P 1 nat polymer 1063.202 PEPTIDE CHAIN P IS A PEPTIDE, CHAIN Q IS A MODEL OF PEPTIDE QL9 DERIVED FROM P 1 nat polymer 424.401 2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose 1 man branched 221.208 2-acetamido-2-deoxy-beta-D-glucopyranose 1 man non-polymer no no GPHSMRYFETAVSRPGLGEPRYISVGYVDNKEFVRFDSDAENPRYEPQAPWMEQEGPEYWERITQIAKGQEQWFRVNLRT LLGYYNQSAGGTHTLQWMYGCDVGSDGRLLRGYEQFAYDGCDYIALNEDLKTWTAADMAAQITRRKWEQAGAAEYYRAYL EGECVEWLHRYLKNGNATLLRTDSPKAHVTHHPRSKGEVTLRCWALGFYPADITLTWQLNGEELTQDMELVETRPAGDGT FQKWASVVVPLGKEQNYTCRVYHEGLPEPLTL GPHSMRYFETAVSRPGLGEPRYISVGYVDNKEFVRFDSDAENPRYEPQAPWMEQEGPEYWERITQIAKGQEQWFRVNLRT LLGYYNQSAGGTHTLQWMYGCDVGSDGRLLRGYEQFAYDGCDYIALNEDLKTWTAADMAAQITRRKWEQAGAAEYYRAYL EGECVEWLHRYLKNGNATLLRTDSPKAHVTHHPRSKGEVTLRCWALGFYPADITLTWQLNGEELTQDMELVETRPAGDGT FQKWASVVVPLGKEQNYTCRVYHEGLPEPLTL H polypeptide(L) no no IQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDWSFYILAHTEFTPTETDTYAC RVKHDSMAEPKTVYWDRDM IQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDWSFYILAHTEFTPTETDTYAC RVKHDSMAEPKTVYWDRDM L polypeptide(L) no no APAAAAAAM APAAAAAAM P polypeptide(L) no no QLSPFPFDL QLSPFPFDL Q polypeptide(L) n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n house mouse Mus fruit fly Drosophila sample MOST NUCLEATED CELLS CYTOPLASM, ER, CELL SURFACE H-2LD 10090 Mus musculus SECRETED 7227 Drosophila melanogaster house mouse Mus fruit fly Drosophila sample MOST NUCLEATED CELLS CYTOPLASM, ER, CELL SURFACE H-2LD 10090 Mus musculus SECRETED 7227 Drosophila melanogaster fruit fly CHAIN P PEPTIDE IS THE NATURAL PRODUCT OF THE EXPRESSION SYSTEM. IT IS ACTUALLY A MODEL REPRESENTING THE ELECTRON DENSITY OF A MIXTURE OF BOUND PEPTIDES AVAILABLE IN THE PROTEIN EXPRESSION MEDIA. Drosophila sample 7227 Drosophila melanogaster fruit fly CHAIN P PEPTIDE IS THE NATURAL PRODUCT OF THE EXPRESSION SYSTEM. IT IS ACTUALLY A MODEL REPRESENTING THE ELECTRON DENSITY OF A MIXTURE OF BOUND PEPTIDES AVAILABLE IN THE PROTEIN EXPRESSION MEDIA. Drosophila sample 7227 Drosophila melanogaster 3 3.18 61. 6.5 PROTEIN WAS CRYSTALLIZED FROM 100MM SODIUM CACODYLATE, 0.2M AMMONIUM SULFATE, 0.5M SODIUM BROMIDE, 30% PEG 8000, PH 6.5. atom_site chem_comp database_PDB_caveat entity pdbx_branch_scheme pdbx_chem_comp_identifier pdbx_entity_branch pdbx_entity_branch_descriptor pdbx_entity_branch_link pdbx_entity_branch_list pdbx_entity_nonpoly pdbx_nonpoly_scheme pdbx_struct_assembly_gen pdbx_validate_chiral struct_asym struct_conn struct_site struct_site_gen chem_comp database_2 pdbx_initial_refinement_model repository Initial release Carbohydrate remediation repository Remediation Version format compliance Version format compliance Advisory Atomic model Data collection Derived calculations Non-polymer description Structure summary Database references Refinement description Structure summary 1 0 1998-06-17 1 1 2008-03-03 1 2 2011-07-13 2 0 2020-07-29 2 1 2023-08-09 _atom_site.B_iso_or_equiv _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.auth_asym_id _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.label_asym_id _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_entity_id _atom_site.type_symbol _chem_comp.formula _chem_comp.formula_weight _chem_comp.id _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.type _pdbx_entity_nonpoly.comp_id _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_struct_assembly_gen.asym_id_list _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_role _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _chem_comp.pdbx_synonyms _database_2.pdbx_DOI _database_2.pdbx_database_accession H NAG 100 n A NAG 1 H NAG 101 n A NDG 2 DGlcpNAcb N-acetyl-b-D-glucopyranosamine b-D-GlcpNAc GlcNAc DGlcpNAca N-acetyl-a-D-glucopyranosamine a-D-GlcpNAc GlcNAc Y BNL 1998-03-15 REL oligosaccharide DGlcpNAca1-4DGlcpNAcb1- 5 GMML 1.0 Glycam Condensed Sequence WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a2122h-1a_1-5_2*NCC/3=O]/1-2/a4-b1 5 PDB2Glycan 1.1.0 WURCS []{[(4+1)][a-D-GlcpNAc]{[(4+1)][a-D-GlcpNAc]{}}} 5 PDB-CARE LINUCS C1 O4 NDG NAG 2 1 5 O1 HO4 sing n n NAG 2-acetamido-2-deoxy-beta-D-glucopyranose 1HOC PDB ENTRY 1HOC PDB experimental model NAG 1 6 NAG NAG 273 H GLY 1 n 1 GLY 1 H PRO 2 n 2 PRO 2 H HIS 3 n 3 HIS 3 H SER 4 n 4 SER 4 H MET 5 n 5 MET 5 H ARG 6 n 6 ARG 6 H TYR 7 n 7 TYR 7 H PHE 8 n 8 PHE 8 H GLU 9 n 9 GLU 9 H THR 10 n 10 THR 10 H ALA 11 n 11 ALA 11 H VAL 12 n 12 VAL 12 H SER 13 n 13 SER 13 H ARG 14 n 14 ARG 14 H PRO 15 n 15 PRO 15 H GLY 16 n 16 GLY 16 H LEU 17 n 17 LEU 17 H GLY 18 n 18 GLY 18 H GLU 19 n 19 GLU 19 H PRO 20 n 20 PRO 20 H ARG 21 n 21 ARG 21 H TYR 22 n 22 TYR 22 H ILE 23 n 23 ILE 23 H SER 24 n 24 SER 24 H VAL 25 n 25 VAL 25 H GLY 26 n 26 GLY 26 H TYR 27 n 27 TYR 27 H VAL 28 n 28 VAL 28 H ASP 29 n 29 ASP 29 H ASN 30 n 30 ASN 30 H LYS 31 n 31 LYS 31 H GLU 32 n 32 GLU 32 H PHE 33 n 33 PHE 33 H VAL 34 n 34 VAL 34 H ARG 35 n 35 ARG 35 H PHE 36 n 36 PHE 36 H ASP 37 n 37 ASP 37 H SER 38 n 38 SER 38 H ASP 39 n 39 ASP 39 H ALA 40 n 40 ALA 40 H GLU 41 n 41 GLU 41 H ASN 42 n 42 ASN 42 H PRO 43 n 43 PRO 43 H ARG 44 n 44 ARG 44 H TYR 45 n 45 TYR 45 H GLU 46 n 46 GLU 46 H PRO 47 n 47 PRO 47 H GLN 48 n 48 GLN 48 H ALA 49 n 49 ALA 49 H PRO 50 n 50 PRO 50 H TRP 51 n 51 TRP 51 H MET 52 n 52 MET 52 H GLU 53 n 53 GLU 53 H GLN 54 n 54 GLN 54 H GLU 55 n 55 GLU 55 H GLY 56 n 56 GLY 56 H PRO 57 n 57 PRO 57 H GLU 58 n 58 GLU 58 H TYR 59 n 59 TYR 59 H TRP 60 n 60 TRP 60 H GLU 61 n 61 GLU 61 H ARG 62 n 62 ARG 62 H ILE 63 n 63 ILE 63 H THR 64 n 64 THR 64 H GLN 65 n 65 GLN 65 H ILE 66 n 66 ILE 66 H ALA 67 n 67 ALA 67 H LYS 68 n 68 LYS 68 H GLY 69 n 69 GLY 69 H GLN 70 n 70 GLN 70 H GLU 71 n 71 GLU 71 H GLN 72 n 72 GLN 72 H TRP 73 n 73 TRP 73 H PHE 74 n 74 PHE 74 H ARG 75 n 75 ARG 75 H VAL 76 n 76 VAL 76 H ASN 77 n 77 ASN 77 H LEU 78 n 78 LEU 78 H ARG 79 n 79 ARG 79 H THR 80 n 80 THR 80 H LEU 81 n 81 LEU 81 H LEU 82 n 82 LEU 82 H GLY 83 n 83 GLY 83 H TYR 84 n 84 TYR 84 H TYR 85 n 85 TYR 85 H ASN 86 n 86 ASN 86 H GLN 87 n 87 GLN 87 H SER 88 n 88 SER 88 H ALA 89 n 89 ALA 89 H GLY 90 n 90 GLY 90 H GLY 91 n 91 GLY 91 H THR 92 n 92 THR 92 H HIS 93 n 93 HIS 93 H THR 94 n 94 THR 94 H LEU 95 n 95 LEU 95 H GLN 96 n 96 GLN 96 H TRP 97 n 97 TRP 97 H MET 98 n 98 MET 98 H TYR 99 n 99 TYR 99 H GLY 100 n 100 GLY 100 H CYS 101 n 101 CYS 101 H ASP 102 n 102 ASP 102 H VAL 103 n 103 VAL 103 H GLY 104 n 104 GLY 104 H SER 105 n 105 SER 105 H ASP 106 n 106 ASP 106 H GLY 107 n 107 GLY 107 H ARG 108 n 108 ARG 108 H LEU 109 n 109 LEU 109 H LEU 110 n 110 LEU 110 H ARG 111 n 111 ARG 111 H GLY 112 n 112 GLY 112 H TYR 113 n 113 TYR 113 H GLU 114 n 114 GLU 114 H GLN 115 n 115 GLN 115 H PHE 116 n 116 PHE 116 H ALA 117 n 117 ALA 117 H TYR 118 n 118 TYR 118 H ASP 119 n 119 ASP 119 H GLY 120 n 120 GLY 120 H CYS 121 n 121 CYS 121 H ASP 122 n 122 ASP 122 H TYR 123 n 123 TYR 123 H ILE 124 n 124 ILE 124 H ALA 125 n 125 ALA 125 H LEU 126 n 126 LEU 126 H ASN 127 n 127 ASN 127 H GLU 128 n 128 GLU 128 H ASP 129 n 129 ASP 129 H LEU 130 n 130 LEU 130 H LYS 131 n 131 LYS 131 H THR 132 n 132 THR 132 H TRP 133 n 133 TRP 133 H THR 134 n 134 THR 134 H ALA 135 n 135 ALA 135 H ALA 136 n 136 ALA 136 H ASP 137 n 137 ASP 137 H MET 138 n 138 MET 138 H ALA 139 n 139 ALA 139 H ALA 140 n 140 ALA 140 H GLN 141 n 141 GLN 141 H ILE 142 n 142 ILE 142 H THR 143 n 143 THR 143 H ARG 144 n 144 ARG 144 H ARG 145 n 145 ARG 145 H LYS 146 n 146 LYS 146 H TRP 147 n 147 TRP 147 H GLU 148 n 148 GLU 148 H GLN 149 n 149 GLN 149 H ALA 150 n 150 ALA 150 H GLY 151 n 151 GLY 151 H ALA 152 n 152 ALA 152 H ALA 153 n 153 ALA 153 H GLU 154 n 154 GLU 154 H TYR 155 n 155 TYR 155 H TYR 156 n 156 TYR 156 H ARG 157 n 157 ARG 157 H ALA 158 n 158 ALA 158 H TYR 159 n 159 TYR 159 H LEU 160 n 160 LEU 160 H GLU 161 n 161 GLU 161 H GLY 162 n 162 GLY 162 H GLU 163 n 163 GLU 163 H CYS 164 n 164 CYS 164 H VAL 165 n 165 VAL 165 H GLU 166 n 166 GLU 166 H TRP 167 n 167 TRP 167 H LEU 168 n 168 LEU 168 H HIS 169 n 169 HIS 169 H ARG 170 n 170 ARG 170 H TYR 171 n 171 TYR 171 H LEU 172 n 172 LEU 172 H LYS 173 n 173 LYS 173 H ASN 174 n 174 ASN 174 H GLY 175 n 175 GLY 175 H ASN 176 n 176 ASN 176 H ALA 177 n 177 ALA 177 H THR 178 n 178 THR 178 H LEU 179 n 179 LEU 179 H LEU 180 n 180 LEU 180 H ARG 181 n 181 ARG 181 H THR 182 n 182 THR 182 H ASP 183 n 183 ASP 183 H SER 184 n 184 SER 184 H PRO 185 n 185 PRO 185 H LYS 186 n 186 LYS 186 H ALA 187 n 187 ALA 187 H HIS 188 n 188 HIS 188 H VAL 189 n 189 VAL 189 H THR 190 n 190 THR 190 H HIS 191 n 191 HIS 191 H HIS 192 n 192 HIS 192 H PRO 193 n 193 PRO 193 H ARG 194 n 194 ARG 194 H SER 195 n 195 SER 195 H LYS 196 n 196 LYS 196 H GLY 197 n 197 GLY 197 H GLU 198 n 198 GLU 198 H VAL 199 n 199 VAL 199 H THR 200 n 200 THR 200 H LEU 201 n 201 LEU 201 H ARG 202 n 202 ARG 202 H CYS 203 n 203 CYS 203 H TRP 204 n 204 TRP 204 H ALA 205 n 205 ALA 205 H LEU 206 n 206 LEU 206 H GLY 207 n 207 GLY 207 H PHE 208 n 208 PHE 208 H TYR 209 n 209 TYR 209 H PRO 210 n 210 PRO 210 H ALA 211 n 211 ALA 211 H ASP 212 n 212 ASP 212 H ILE 213 n 213 ILE 213 H THR 214 n 214 THR 214 H LEU 215 n 215 LEU 215 H THR 216 n 216 THR 216 H TRP 217 n 217 TRP 217 H GLN 218 n 218 GLN 218 H LEU 219 n 219 LEU 219 H ASN 220 n 220 ASN 220 H GLY 221 n 221 GLY 221 H GLU 222 n 222 GLU 222 H GLU 223 n 223 GLU 223 H LEU 224 n 224 LEU 224 H THR 225 n 225 THR 225 H GLN 226 n 226 GLN 226 H ASP 227 n 227 ASP 227 H MET 228 n 228 MET 228 H GLU 229 n 229 GLU 229 H LEU 230 n 230 LEU 230 H VAL 231 n 231 VAL 231 H GLU 232 n 232 GLU 232 H THR 233 n 233 THR 233 H ARG 234 n 234 ARG 234 H PRO 235 n 235 PRO 235 H ALA 236 n 236 ALA 236 H GLY 237 n 237 GLY 237 H ASP 238 n 238 ASP 238 H GLY 239 n 239 GLY 239 H THR 240 n 240 THR 240 H PHE 241 n 241 PHE 241 H GLN 242 n 242 GLN 242 H LYS 243 n 243 LYS 243 H TRP 244 n 244 TRP 244 H ALA 245 n 245 ALA 245 H SER 246 n 246 SER 246 H VAL 247 n 247 VAL 247 H VAL 248 n 248 VAL 248 H VAL 249 n 249 VAL 249 H PRO 250 n 250 PRO 250 H LEU 251 n 251 LEU 251 H GLY 252 n 252 GLY 252 H LYS 253 n 253 LYS 253 H GLU 254 n 254 GLU 254 H GLN 255 n 255 GLN 255 H ASN 256 n 256 ASN 256 H TYR 257 n 257 TYR 257 H THR 258 n 258 THR 258 H CYS 259 n 259 CYS 259 H ARG 260 n 260 ARG 260 H VAL 261 n 261 VAL 261 H TYR 262 n 262 TYR 262 H HIS 263 n 263 HIS 263 H GLU 264 n 264 GLU 264 H GLY 265 n 265 GLY 265 H LEU 266 n 266 LEU 266 H PRO 267 n 267 PRO 267 H GLU 268 n 268 GLU 268 H PRO 269 n 269 PRO 269 H LEU 270 n 270 LEU 270 H THR 271 n 271 THR 271 H LEU 272 n 272 LEU 272 H ILE 1 n 1 ILE 1 L GLN 2 n 2 GLN 2 L LYS 3 n 3 LYS 3 L THR 4 n 4 THR 4 L PRO 5 n 5 PRO 5 L GLN 6 n 6 GLN 6 L ILE 7 n 7 ILE 7 L GLN 8 n 8 GLN 8 L VAL 9 n 9 VAL 9 L TYR 10 n 10 TYR 10 L SER 11 n 11 SER 11 L ARG 12 n 12 ARG 12 L HIS 13 n 13 HIS 13 L PRO 14 n 14 PRO 14 L PRO 15 n 15 PRO 15 L GLU 16 n 16 GLU 16 L ASN 17 n 17 ASN 17 L GLY 18 n 18 GLY 18 L LYS 19 n 19 LYS 19 L PRO 20 n 20 PRO 20 L ASN 21 n 21 ASN 21 L ILE 22 n 22 ILE 22 L LEU 23 n 23 LEU 23 L ASN 24 n 24 ASN 24 L CYS 25 n 25 CYS 25 L TYR 26 n 26 TYR 26 L VAL 27 n 27 VAL 27 L THR 28 n 28 THR 28 L GLN 29 n 29 GLN 29 L PHE 30 n 30 PHE 30 L HIS 31 n 31 HIS 31 L PRO 32 n 32 PRO 32 L PRO 33 n 33 PRO 33 L HIS 34 n 34 HIS 34 L ILE 35 n 35 ILE 35 L GLU 36 n 36 GLU 36 L ILE 37 n 37 ILE 37 L GLN 38 n 38 GLN 38 L MET 39 n 39 MET 39 L LEU 40 n 40 LEU 40 L LYS 41 n 41 LYS 41 L ASN 42 n 42 ASN 42 L GLY 43 n 43 GLY 43 L LYS 44 n 44 LYS 44 L LYS 45 n 45 LYS 45 L ILE 46 n 46 ILE 46 L PRO 47 n 47 PRO 47 L LYS 48 n 48 LYS 48 L VAL 49 n 49 VAL 49 L GLU 50 n 50 GLU 50 L MET 51 n 51 MET 51 L SER 52 n 52 SER 52 L ASP 53 n 53 ASP 53 L MET 54 n 54 MET 54 L SER 55 n 55 SER 55 L PHE 56 n 56 PHE 56 L SER 57 n 57 SER 57 L LYS 58 n 58 LYS 58 L ASP 59 n 59 ASP 59 L TRP 60 n 60 TRP 60 L SER 61 n 61 SER 61 L PHE 62 n 62 PHE 62 L TYR 63 n 63 TYR 63 L ILE 64 n 64 ILE 64 L LEU 65 n 65 LEU 65 L ALA 66 n 66 ALA 66 L HIS 67 n 67 HIS 67 L THR 68 n 68 THR 68 L GLU 69 n 69 GLU 69 L PHE 70 n 70 PHE 70 L THR 71 n 71 THR 71 L PRO 72 n 72 PRO 72 L THR 73 n 73 THR 73 L GLU 74 n 74 GLU 74 L THR 75 n 75 THR 75 L ASP 76 n 76 ASP 76 L THR 77 n 77 THR 77 L TYR 78 n 78 TYR 78 L ALA 79 n 79 ALA 79 L CYS 80 n 80 CYS 80 L ARG 81 n 81 ARG 81 L VAL 82 n 82 VAL 82 L LYS 83 n 83 LYS 83 L HIS 84 n 84 HIS 84 L ASP 85 n 85 ASP 85 L SER 86 n 86 SER 86 L MET 87 n 87 MET 87 L ALA 88 n 88 ALA 88 L GLU 89 n 89 GLU 89 L PRO 90 n 90 PRO 90 L LYS 91 n 91 LYS 91 L THR 92 n 92 THR 92 L VAL 93 n 93 VAL 93 L TYR 94 n 94 TYR 94 L TRP 95 n 95 TRP 95 L ASP 96 n 96 ASP 96 L ARG 97 n 97 ARG 97 L ASP 98 n 98 ASP 98 L MET 99 n 99 MET 99 L ALA 1 n 1 ALA 1 P PRO 2 n 2 PRO 2 P ALA 3 n 3 ALA 3 P ALA 4 n 4 ALA 4 P ALA 5 n 5 ALA 5 P ALA 6 n 6 ALA 6 P ALA 7 n 7 ALA 7 P ALA 8 n 8 ALA 8 P MET 9 n 9 MET 9 P GLN 1 n 1 GLN 1 Q LEU 2 n 2 LEU 2 Q SER 3 n 3 SER 3 Q PRO 4 n 4 PRO 4 Q PHE 5 n 5 PHE 5 Q PRO 6 n 6 PRO 6 Q PHE 7 n 7 PHE 7 Q ASP 8 n 8 ASP 8 Q LEU 9 n 9 LEU 9 Q author_defined_assembly 4 tetrameric H ASN 86 GLYCOSYLATION SITE A ASN 86 ASN H ASN 176 GLYCOSYLATION SITE A ASN 176 ASN 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 x,y,z identity operation 0.0000000000 0.0000000000 0.0000000000 H O LYS 31 A O LYS 31 H N VAL 28 A N VAL 28 H O TYR 27 A O TYR 27 H N ARG 6 A N ARG 6 H O HIS 3 A O HIS 3 H N VAL 103 A N VAL 103 H O GLN 96 A O GLN 96 H N ALA 117 A N ALA 117 H O PHE 116 A O PHE 116 H N ILE 124 A N ILE 124 H O THR 214 A O THR 214 H N TYR 262 A N TYR 262 H O VAL 199 A O VAL 199 H N VAL 249 A N VAL 249 L O LEU 23 B O LEU 23 L N THR 68 B N THR 68 L O GLU 36 B O GLU 36 L N LYS 83 B N LYS 83 L O CYS 80 B O CYS 80 L N VAL 93 B N VAL 93 1 A C1 NAG 1 WRONG HAND 1 H C1 NAG 273 WRONG HAND 1 P Q O O PRO LEU 2 2 0.12 1 P Q CA CA ALA ASP 8 8 0.14 1 P Q CB CB ALA SER 3 3 0.14 1 P Q C C PRO LEU 2 2 0.15 1 P Q CA CA PRO LEU 2 2 0.15 1 P Q CA CA ALA SER 3 3 0.16 1 P Q N N ALA SER 3 3 0.16 1 P Q N N ALA ASP 8 8 0.17 1 P Q N N ALA PHE 7 7 0.19 1 P Q C C ALA PHE 7 7 0.19 1 P Q C C ALA SER 3 3 0.20 1 P Q N N MET LEU 9 9 0.22 1 P Q C C ALA GLN 1 1 0.23 1 P Q O O ALA GLN 1 1 0.23 1 P Q O O ALA PRO 4 4 0.23 1 P Q CA CA ALA GLN 1 1 0.24 1 P Q CA CA ALA PHE 7 7 0.25 1 P Q N N PRO LEU 2 2 0.26 1 P Q CB CB ALA GLN 1 1 0.27 1 P Q O O ALA PHE 7 7 0.28 1 P Q N N ALA PRO 4 4 0.28 1 P Q C C ALA PRO 6 6 0.29 1 P Q O O ALA SER 3 3 0.31 1 P Q C C ALA PRO 4 4 0.32 1 P Q CA CA ALA PRO 4 4 0.32 1 P Q O O ALA PRO 6 6 0.32 1 P Q CB CB ALA PRO 4 4 0.40 1 P Q CB CB ALA ASP 8 8 0.41 1 P Q CB CB ALA PRO 6 6 0.44 1 P Q N N ALA PRO 6 6 0.45 1 P Q CA CA MET LEU 9 9 0.45 1 P Q CA CA ALA PRO 6 6 0.46 1 P Q C C ALA ASP 8 8 0.46 1 P Q C C ALA PHE 5 5 0.53 1 P Q CB CB ALA PHE 7 7 0.54 1 P Q O O MET LEU 9 9 0.54 1 P Q C C MET LEU 9 9 0.55 1 P Q CG CG MET LEU 9 9 0.56 1 P Q CB CB MET LEU 9 9 0.57 1 P Q O O ALA PHE 5 5 0.58 1 P Q N N ALA PHE 5 5 0.58 1 P Q CA CA ALA PHE 5 5 0.62 1 P Q CB CB PRO LEU 2 2 0.63 1 P Q N N ALA GLN 1 1 0.64 1 P Q OXT OXT MET LEU 9 9 0.69 1 P Q CB CB ALA PHE 5 5 0.73 1 P Q CB CG ALA PHE 5 5 0.75 1 P Q O C MET LEU 9 9 0.79 1 P Q SD CD2 MET LEU 9 9 0.89 1 P Q O O ALA ASP 8 8 0.92 1 P Q C O ALA PRO 4 4 1.01 1 P Q C O ALA GLN 1 1 1.02 1 P Q O C ALA PHE 5 5 1.03 1 P Q O C ALA PRO 6 6 1.04 1 P Q CA N ALA PRO 6 6 1.05 1 P Q CB CG ALA PRO 6 6 1.05 1 P Q C O ALA SER 3 3 1.09 1 P Q CG CD2 MET LEU 9 9 1.11 1 P Q N C ALA SER 4 3 1.15 1 P Q C CA MET LEU 9 9 1.15 1 P Q N C PRO GLN 2 1 1.15 1 P Q O C PRO LEU 2 2 1.15 1 P Q C CA ALA PHE 5 5 1.17 1 P Q O C ALA PHE 7 7 1.18 1 P Q N C ALA PHE 8 7 1.21 1 P Q CB CG PRO LEU 2 2 1.23 1 P Q CB CA ALA PRO 4 4 1.24 1 P Q CB CG ALA GLN 1 1 1.27 1 P Q CB CG ALA PHE 7 7 1.28 1 P Q C N ALA LEU 8 9 1.28 1 P Q CA CB MET LEU 9 9 1.28 1 P Q N CA ALA PHE 5 5 1.28 1 P Q N CD ALA PRO 6 6 1.29 1 P Q C O ALA PHE 7 7 1.29 1 P Q CA N ALA PHE 7 7 1.29 1 P Q C CA ALA PRO 6 6 1.30 1 P Q CA CB ALA PHE 5 5 1.30 1 P Q N C ALA PHE 6 5 1.30 1 P Q N C ALA LEU 3 2 1.31 1 P Q C OXT MET LEU 9 9 1.32 1 P Q CA N ALA SER 3 3 1.32 1 P Q C O PRO LEU 2 2 1.33 1 P Q CA N ALA ASP 8 8 1.33 1 P Q N C ALA PRO 7 6 1.35 1 P Q O C ALA ASP 8 8 1.35 1 P Q C CA ALA PHE 7 7 1.35 1 P Q CA C ALA PRO 4 4 1.36 1 P Q CA CB ALA GLN 1 1 1.36 1 P Q C CA PRO LEU 2 2 1.36 1 P Q N C ALA PRO 5 4 1.36 1 P Q C N ALA PHE 6 7 1.37 1 P Q C N PRO SER 2 3 1.37 1 P Q CD N PRO LEU 2 2 1.38 1 P Q CB CA ALA ASP 8 8 1.38 1 P Q O C ALA SER 3 3 1.41 1 P Q CA N PRO LEU 2 2 1.42 1 P Q C N ALA ASP 7 8 1.43 1 P Q C N ALA PHE 4 5 1.43 1 P Q O C ALA GLN 1 1 1.44 1 P Q C O ALA ASP 8 8 1.44 1 P Q N C MET ASP 9 8 1.44 1 P Q CA CB PRO LEU 2 2 1.45 1 P Q CB CA ALA SER 3 3 1.45 1 P Q CA N ALA PRO 4 4 1.45 1 P Q OXT C MET LEU 9 9 1.46 1 P Q CA N ALA GLN 1 1 1.46 1 P Q CB CA ALA PHE 7 7 1.47 1 P Q CB OG ALA SER 3 3 1.47 1 P Q O C ALA PRO 4 4 1.48 1 P Q C O ALA PRO 6 6 1.48 1 P Q CA N MET LEU 9 9 1.48 1 P Q N CA PRO LEU 2 2 1.50 1 P Q CG CB MET LEU 9 9 1.50 1 P Q N CA MET LEU 9 9 1.52 1 P Q C CA ALA SER 3 3 1.52 1 P Q CA C ALA GLN 1 1 1.53 1 P Q C N ALA PRO 3 4 1.53 1 P Q C CA ALA ASP 8 8 1.53 1 P Q N CA ALA PRO 4 4 1.53 1 P Q N CA ALA ASP 8 8 1.53 1 P Q C N ALA LEU 1 2 1.53 1 P Q C N ALA PRO 5 6 1.53 1 P Q C CA ALA GLN 1 1 1.54 1 P Q CA C ALA ASP 8 8 1.54 1 P Q CA C ALA SER 3 3 1.56 1 P Q CA CB ALA PRO 6 6 1.56 1 P Q N CA ALA GLN 1 1 1.58 1 P Q C O ALA PHE 5 5 1.60 1 P Q CB CA PRO LEU 2 2 1.61 1 P Q N CA ALA SER 3 3 1.62 1 P Q CA CB ALA SER 3 3 1.62 1 P Q CG CD2 PRO LEU 2 2 1.62 1 P Q N CA ALA PHE 7 7 1.64 1 P Q CA CB ALA ASP 8 8 1.64 1 P Q CA C PRO LEU 2 2 1.65 1 P Q CB CA ALA PRO 6 6 1.65 1 P Q CA CB ALA PHE 7 7 1.66 1 P Q CB CA ALA GLN 1 1 1.68 1 P Q CB CG MET LEU 9 9 1.70 1 P Q CA C ALA PHE 7 7 1.71 1 P Q N CD ALA PRO 4 4 1.72 1 P Q C O MET LEU 9 9 1.75 1 P Q C CA ALA PRO 4 4 1.77 1 P Q CA N ALA PHE 5 5 1.82 1 P Q CB CD1 ALA PHE 5 5 1.83 1 P Q CA CB ALA PRO 4 4 1.84 1 H Q NH2 OE1 ARG GLN 62 1 1.84 1 P Q CA C ALA PRO 6 6 1.85 1 P Q CB CG ALA PRO 4 4 1.85 1 P Q CG CD1 MET LEU 9 9 1.85 1 P Q O OXT MET LEU 9 9 1.85 1 P Q CB CA MET LEU 9 9 1.89 1 P Q CB CD2 ALA PHE 5 5 1.89 1 P Q N CA ALA PRO 6 6 1.90 1 P Q CB CG ALA ASP 8 8 1.92 1 P Q CG CB PRO LEU 2 2 1.92 1 P Q CB CA ALA PHE 5 5 1.94 1 P Q CB CD2 PRO LEU 2 2 1.94 1 P Q CA CG ALA PHE 5 5 1.94 1 P Q CE CD2 MET LEU 9 9 1.96 1 P Q O CA MET LEU 9 9 1.97 1 P Q CA CD ALA PRO 6 6 1.97 1 P Q CA C MET LEU 9 9 1.98 1 P Q CA C ALA PHE 5 5 1.98 1 P Q O CA ALA PHE 5 5 2.00 1 P Q C CB MET LEU 9 9 2.02 1 P Q CB CD ALA PRO 6 6 2.03 1 P Q N O PRO GLN 2 1 2.03 1 P Q N O ALA SER 4 3 2.04 1 P Q N CB ALA PHE 5 5 2.05 1 P Q N O ALA PRO 5 4 2.06 1 P Q CB CD1 ALA PHE 7 7 2.06 1 P Q C CB ALA PHE 5 5 2.07 1 H Q OH CZ TYR PHE 156 5 2.08 1 P Q O CA ALA PRO 6 6 2.10 1 P Q CA CG ALA PRO 6 6 2.12 1 P Q OXT CA MET LEU 9 9 2.12 1 P Q CG CG PRO LEU 2 2 2.13 1 P Q N O ALA PHE 8 7 2.14 1 P Q N CA ALA PHE 6 5 2.16 1 P Q CA C ALA PHE 6 5 2.17 1 P Q CB N PRO LEU 2 2 2.18 1 P Q O N ALA LEU 8 9 2.19 1 P Q C N ALA PRO 6 6 2.19 1 H H O ND2 ARG ASN 170 174 2.19 1 9.71 1.50 119.30 129.01 H H H C N CA GLY PRO PRO 56 57 57 Y 1 9.66 1.50 119.30 128.96 H H H C N CA ARG PRO PRO 234 235 235 Y 1 9.22 1.50 119.30 128.52 P P P C N CA ALA PRO PRO 1 2 2 Y 1 H PRO 2 -46.66 163.53 1 H PRO 15 -34.98 -71.49 1 H GLU 19 -170.84 140.87 1 H ARG 21 -104.33 67.56 1 H ASP 29 60.31 65.52 1 H ASN 30 59.57 2.97 1 H ASP 37 -167.69 89.56 1 H SER 38 -58.56 26.77 1 H GLN 48 -99.70 -60.14 1 H TRP 51 -59.68 -2.16 1 H GLN 54 -62.37 10.89 1 H THR 64 -43.68 -17.51 1 H ASN 77 -51.31 -77.29 1 H LEU 78 -26.07 -37.98 1 H ASN 86 33.82 45.17 1 H ALA 89 -50.71 90.73 1 H THR 94 -160.54 105.79 1 H ASP 119 81.05 24.84 1 H ASP 129 -52.76 -6.42 1 H LEU 160 -50.79 -74.94 1 H HIS 188 -172.22 133.36 1 H SER 195 -44.96 -9.89 1 H PRO 210 -65.26 -174.50 1 H ASP 212 -48.44 100.36 1 H LEU 219 -174.00 92.15 1 H ASN 220 58.85 71.26 1 H LEU 224 -67.73 52.38 1 H THR 233 -42.65 108.53 1 H PHE 241 -100.65 -163.43 1 H GLN 255 -37.40 -21.84 1 H GLU 264 -69.37 87.96 1 H PRO 269 -39.35 151.10 1 L TYR 10 179.05 158.05 1 L ASN 17 -23.69 115.08 1 L PRO 20 -50.99 103.30 1 L CYS 25 -160.31 75.86 1 L HIS 31 -178.88 130.82 1 L PRO 33 -43.24 -15.36 1 L LYS 41 -167.51 110.13 1 L MET 54 -58.89 85.68 1 L ASP 59 -68.96 8.99 1 L GLU 74 -37.11 -22.02 1 L HIS 84 -162.07 119.72 1 L ASP 85 -26.03 -40.64 1 L SER 86 -72.40 41.91 1 L MET 87 -176.51 141.65 1 L ARG 97 -21.15 -58.59 1 P ALA 7 -54.64 106.43 1 Q PHE 7 -43.92 99.79 PARHCSDX.PRO TOPHCSDX.PRO PARAM3_MOD.CHO TOPH3.CHO TOPH19SYED.PEP 28. -4.192 0. -6.204 2.918 0. 1.274 SOME LIBRARIES WERE MODIFIED IN-HOUSE TO PROVIDE MISSING CARBOHYDRATE AND PROTEIN SPECIFICATIONS. X-PLOR 3.1 ALSO WAS USED. 0.371 0.016 0.221 0.221 3.1 6.0 556 7935 6. 85. RANDOM 100000. 0.1 1 ONE B-VALUE PER RESIDUE THROUGHOUT 1. MOLECULAR REPLACEMENT PDB ENTRY 1HOC 0.60 0.35 6.0 3.1 6.0 0 3129 42 0 3087 0.015 1.8 25.8 1.8 0.477 0.062 0.291 3.22 59 783 8 10.6 72. 2.8 15. 1LDP 11809 0. 0.113 0.113 1 5.6 2.2 81. 0.358 2.8 2.9 1.8 0.358 1.4 63.6 data scaling XDS data scaling SCALEPACK model building X-PLOR refinement X-PLOR 3.825 data reduction XDS phasing X-PLOR CRYSTAL STRUCTURE OF MURINE MHC CLASS I H-2LD WITH A MIXTURE OF BOUND PEPTIDES 1 N N 2 N N 3 N N 4 N N 5 N N 6 N N H PRO 57 A PRO 57 HELX_P H TYR 84 A TYR 84 1 1 28 H MET 138 A MET 138 HELX_P H ALA 150 A ALA 150 1 2 13 H ALA 152 A ALA 152 HELX_P H GLU 161 A GLU 161 1 3 10 H GLU 163 A GLU 163 HELX_P H ASN 174 A ASN 174 1 4 12 H ASN 176 A ASN 176 HELX_P H LEU 179 A LEU 179 1 5 4 H GLU 254 A GLU 254 HELX_P H ASN 256 A ASN 256 5 6 3 disulf 2.002 H CYS 101 A SG CYS 101 1_555 H CYS 164 A SG CYS 164 1_555 disulf 2.033 H CYS 203 A SG CYS 203 1_555 H CYS 259 A SG CYS 259 1_555 disulf 2.011 L CYS 25 B SG CYS 25 1_555 L CYS 80 B SG CYS 80 1_555 covale 1.495 one N-Glycosylation H ASN 86 A ND2 ASN 86 1_555 H NAG 273 F C1 NAG 1_555 covale 1.450 one N-Glycosylation H ASN 176 A ND2 ASN 176 1_555 A NAG 1 E C1 NAG 1_555 covale 1.438 both A NAG 1 E O4 NAG 1_555 A NDG 2 E C1 NDG 1_555 COMPLEX (MHC I/PEPTIDE) COMPLEX (MHC I-PEPTIDE), MAJOR HISTOCOMPATIBILITY COMPLEX, IMMUNOLOGY, CELLULAR IMMUNITY, PEPTIDE ANTIGEN, CELL SURFACE RECEPTOR, ANTIGEN RECEPTOR, ANTIGEN PRESENTATION, COMPLEX (MHC I-PEPTIDE) complex H TYR 209 A TYR 209 1 H PRO 210 A PRO 210 0.38 L HIS 31 B HIS 31 1 L PRO 32 B PRO 32 -1.91 HA1L_MOUSE UNP 1 1 P01897 MGAMAPRTLLLLLAAALAPTQTRAGPHSMRYFETAVSRPGLGEPRYISVGYVDNKEFVRFDSDAENPRYEPQAPWMEQEG PEYWERITQIAKGQEQWFRVNLRTLLGYYNQSAGGTHTLQWMYGCDVGSDGRLLRGYEQFAYDGCDYIALNEDLKTWTAA DMAAQITRRKWEQAGAAEYYRAYLEGECVEWLHRYLKNGNATLLRTDSPKAHVTHHPRSKGEVTLRCWALGFYPADITLT WQLNGEELTQDMELVETRPAGDGTFQKWASVVVPLGKEQNYTCRVYHEGLPEPLTLRWEPPPSTDSYMVIVAVLGVLGAM AIIGAVVAFVMKRRRNTGGKGGDYALAPGSQSSEMSLRDCKA B2MG_MOUSE UNP 2 1 P01887 MARSVTLVFLVLVSLTGLYAIQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDW SFYILAHTEFTPTETDTYACRVKHDSMAEPKTVYWDRDM 1LDP PDB 3 1LDP 1LDP PDB 4 1LDP 25 296 1LDP 1 272 P01897 H 1 1 272 21 119 1LDP 1 99 P01887 L 2 1 99 1 9 1LDP 1 9 1LDP P 3 1 9 1 9 1LDP 1 9 1LDP Q 4 1 9 6 2 2 2 3 anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel H LYS 31 A LYS 31 H ARG 35 A ARG 35 H VAL 25 A VAL 25 H VAL 28 A VAL 28 H HIS 3 A HIS 3 H VAL 12 A VAL 12 H THR 94 A THR 94 H VAL 103 A VAL 103 H LEU 109 A LEU 109 H TYR 118 A TYR 118 H ASP 122 A ASP 122 H ALA 125 A ALA 125 H ILE 213 A ILE 213 H GLN 218 A GLN 218 H THR 258 A THR 258 H HIS 263 A HIS 263 H GLU 198 A GLU 198 H PHE 208 A PHE 208 H PHE 241 A PHE 241 H PRO 250 A PRO 250 L LEU 23 B LEU 23 L TYR 26 B TYR 26 L LEU 65 B LEU 65 L THR 68 B THR 68 L ILE 35 B ILE 35 L LYS 41 B LYS 41 L TYR 78 B TYR 78 L HIS 84 B HIS 84 L LYS 91 B LYS 91 L TYR 94 B TYR 94 THIS NINE AMINO ACID MODEL BEST FITS THE ELECTRON DENSITY REPRESENTING A MIXTURE OF PEPTIDES BOUND IN THE H-2LD PEPTIDE-BINDING GROOVE. IT WAS USED THROUGHOUT H-2LD REFINEMENT. Unknown 1 THIS NINE RESIDUE MODEL OF ANTIGENIC PEPTIDE QL9 ALSO FITS WELL TO THE ELECTRON DENSITY OF THE H-2LD BOUND PEPTIDE MIXTURE. THESE COORDINATES HAVE BEEN REFINED IN X-PLOR TOGETHER WITH THE FINAL MODELS OF THE H AND L CHAINS. Unknown 1 P ALA 1 C ALA 1 1 1_555 Q GLN 1 D GLN 1 1 1_555 3 P 1 2 1