0.012747 0.007359 0.000000 0.000000 0.014719 0.000000 0.000000 0.000000 0.006285 0.00000 0.00000 0.00000 Ghosh, P. Amaya, M. Mellins, E. Wiley, D.C. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 6 90.00 90.00 120.00 78.450 78.450 159.100 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 H2 O 18.015 WATER non-polymer 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 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 UK Nature NATUAS 0006 0028-0836 378 457 462 10.1038/378457a0 7477400 The structure of an intermediate in class II MHC maturation: CLIP bound to HLA-DR3. 1995 10.2210/pdb1a6a/pdb pdb_00001a6a 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 100 1 MIRRORS IMAGE PLATE 1994-07 FUJI SI(111) M x-ray 1 0.918 1.0 F1 CHESS 0.918 SYNCHROTRON CHESS BEAMLINE F1 20469.172 HLA class II histocompatibility antigen, DR alpha chain 1 nat polymer 21935.385 HLA class II histocompatibility antigen, DR-1 beta chain 1 nat polymer 1676.118 HLA class II histocompatibility antigen, gamma chain CLIP FRAGMENT 87 - 101 OF INVARIANT CHAIN 1 nat polymer 221.208 2-acetamido-2-deoxy-beta-D-glucopyranose 2 man non-polymer 18.015 water 22 nat water no no HVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGALANIAVDKANLEIMTKRSNYTPITN VPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVTWLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCR VEHWGLDEPLLKHWEF HVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGALANIAVDKANLEIMTKRSNYTPITN VPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVTWLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCR VEHWGLDEPLLKHWEF A polypeptide(L) no no PRFLEYSTSECHFFNGTERVRYLDRYFHNQEENVRFDSDVGEFRAVTELGRPDAEYWNSQKDLLEQKRGRVDNYCRHNYG VVESFTVQRRVHPKVTVYPSKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKTGVVSTGLIHNGDWTFQTLVMLETV PRSGEVYTCQVEHPSVTSPLTVEWRAR PRFLEYSTSECHFFNGTERVRYLDRYFHNQEENVRFDSDVGEFRAVTELGRPDAEYWNSQKDLLEQKRGRVDNYCRHNYG VVESFTVQRRVHPKVTVYPSKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKTGVVSTGLIHNGDWTFQTLVMLETV PRSGEVYTCQVEHPSVTSPLTVEWRAR B polypeptide(L) no no PVSKMRMATPLLMQA PVSKMRMATPLLMQA C 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 human Homo sample B-LYMPHOCYTE 9.5.3 PLASMA MEMBRANE 9606 Homo sapiens human Homo sample B-LYMPHOCYTE 9.5.3 PLASMA MEMBRANE 9606 Homo sapiens human Homo sample B-LYMPHOCYTE 9.5.3 PLASMA MEMBRANE 9606 Homo sapiens 2 2.7 52. 4.5 12% PEG 4K, 100 MM MGCL2, 100 MM ACETATE BUFFER, PH 4.5 chem_comp entity pdbx_chem_comp_identifier pdbx_entity_nonpoly pdbx_unobs_or_zero_occ_atoms software struct_conn struct_site struct_site_gen chem_comp database_2 pdbx_initial_refinement_model pdbx_unobs_or_zero_occ_atoms repository Initial release Carbohydrate remediation repository Remediation Version format compliance Non-polymer description Version format compliance Advisory Data collection Derived calculations Refinement description Structure summary Advisory Database references Refinement description Structure summary 1 0 1998-05-27 1 1 2008-03-24 1 2 2011-07-13 1 3 2020-07-29 1 4 2023-08-02 _chem_comp.name _chem_comp.type _entity.pdbx_description _pdbx_entity_nonpoly.name _software.name _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_role _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_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 DGlcpNAcb N-acetyl-b-D-glucopyranosamine b-D-GlcpNAc GlcNAc Y BNL 1998-02-22 REL REL NAG 2-acetamido-2-deoxy-beta-D-glucopyranose HOH water 1DLH PDB ENTRY 1DLH PDB experimental model NAG 100 4 NAG NAG 181 A NAG 200 4 NAG NAG 200 A HOH 6 5 HOH HOH 201 A HOH 8 5 HOH HOH 202 A HOH 9 5 HOH HOH 203 A HOH 16 5 HOH HOH 204 A HOH 17 5 HOH HOH 205 A HOH 20 5 HOH HOH 206 A HOH 21 5 HOH HOH 207 A HOH 22 5 HOH HOH 208 A HOH 1 5 HOH HOH 192 B HOH 2 5 HOH HOH 193 B HOH 3 5 HOH HOH 194 B HOH 4 5 HOH HOH 195 B HOH 5 5 HOH HOH 196 B HOH 7 5 HOH HOH 197 B HOH 11 5 HOH HOH 198 B HOH 12 5 HOH HOH 199 B HOH 13 5 HOH HOH 200 B HOH 14 5 HOH HOH 201 B HOH 15 5 HOH HOH 202 B HOH 18 5 HOH HOH 203 B HOH 19 5 HOH HOH 204 B HOH 10 5 HOH HOH 10 C HIS 5 n 1 HIS 5 A VAL 6 n 2 VAL 6 A ILE 7 n 3 ILE 7 A ILE 8 n 4 ILE 8 A GLN 9 n 5 GLN 9 A ALA 10 n 6 ALA 10 A GLU 11 n 7 GLU 11 A PHE 12 n 8 PHE 12 A TYR 13 n 9 TYR 13 A LEU 14 n 10 LEU 14 A ASN 15 n 11 ASN 15 A PRO 16 n 12 PRO 16 A ASP 17 n 13 ASP 17 A GLN 18 n 14 GLN 18 A SER 19 n 15 SER 19 A GLY 20 n 16 GLY 20 A GLU 21 n 17 GLU 21 A PHE 22 n 18 PHE 22 A MET 23 n 19 MET 23 A PHE 24 n 20 PHE 24 A ASP 25 n 21 ASP 25 A PHE 26 n 22 PHE 26 A ASP 27 n 23 ASP 27 A GLY 28 n 24 GLY 28 A ASP 29 n 25 ASP 29 A GLU 30 n 26 GLU 30 A ILE 31 n 27 ILE 31 A PHE 32 n 28 PHE 32 A HIS 33 n 29 HIS 33 A VAL 34 n 30 VAL 34 A ASP 35 n 31 ASP 35 A MET 36 n 32 MET 36 A ALA 37 n 33 ALA 37 A LYS 38 n 34 LYS 38 A LYS 39 n 35 LYS 39 A GLU 40 n 36 GLU 40 A THR 41 n 37 THR 41 A VAL 42 n 38 VAL 42 A TRP 43 n 39 TRP 43 A ARG 44 n 40 ARG 44 A LEU 45 n 41 LEU 45 A GLU 46 n 42 GLU 46 A GLU 47 n 43 GLU 47 A PHE 48 n 44 PHE 48 A GLY 49 n 45 GLY 49 A ARG 50 n 46 ARG 50 A PHE 51 n 47 PHE 51 A ALA 52 n 48 ALA 52 A SER 53 n 49 SER 53 A PHE 54 n 50 PHE 54 A GLU 55 n 51 GLU 55 A ALA 56 n 52 ALA 56 A GLN 57 n 53 GLN 57 A GLY 58 n 54 GLY 58 A ALA 59 n 55 ALA 59 A LEU 60 n 56 LEU 60 A ALA 61 n 57 ALA 61 A ASN 62 n 58 ASN 62 A ILE 63 n 59 ILE 63 A ALA 64 n 60 ALA 64 A VAL 65 n 61 VAL 65 A ASP 66 n 62 ASP 66 A LYS 67 n 63 LYS 67 A ALA 68 n 64 ALA 68 A ASN 69 n 65 ASN 69 A LEU 70 n 66 LEU 70 A GLU 71 n 67 GLU 71 A ILE 72 n 68 ILE 72 A MET 73 n 69 MET 73 A THR 74 n 70 THR 74 A LYS 75 n 71 LYS 75 A ARG 76 n 72 ARG 76 A SER 77 n 73 SER 77 A ASN 78 n 74 ASN 78 A TYR 79 n 75 TYR 79 A THR 80 n 76 THR 80 A PRO 81 n 77 PRO 81 A ILE 82 n 78 ILE 82 A THR 83 n 79 THR 83 A ASN 84 n 80 ASN 84 A VAL 85 n 81 VAL 85 A PRO 86 n 82 PRO 86 A PRO 87 n 83 PRO 87 A GLU 88 n 84 GLU 88 A VAL 89 n 85 VAL 89 A THR 90 n 86 THR 90 A VAL 91 n 87 VAL 91 A LEU 92 n 88 LEU 92 A THR 93 n 89 THR 93 A ASN 94 n 90 ASN 94 A SER 95 n 91 SER 95 A PRO 96 n 92 PRO 96 A VAL 97 n 93 VAL 97 A GLU 98 n 94 GLU 98 A LEU 99 n 95 LEU 99 A ARG 100 n 96 ARG 100 A GLU 101 n 97 GLU 101 A PRO 102 n 98 PRO 102 A ASN 103 n 99 ASN 103 A VAL 104 n 100 VAL 104 A LEU 105 n 101 LEU 105 A ILE 106 n 102 ILE 106 A CYS 107 n 103 CYS 107 A PHE 108 n 104 PHE 108 A ILE 109 n 105 ILE 109 A ASP 110 n 106 ASP 110 A LYS 111 n 107 LYS 111 A PHE 112 n 108 PHE 112 A THR 113 n 109 THR 113 A PRO 114 n 110 PRO 114 A PRO 115 n 111 PRO 115 A VAL 116 n 112 VAL 116 A VAL 117 n 113 VAL 117 A ASN 118 n 114 ASN 118 A VAL 119 n 115 VAL 119 A THR 120 n 116 THR 120 A TRP 121 n 117 TRP 121 A LEU 122 n 118 LEU 122 A ARG 123 n 119 ARG 123 A ASN 124 n 120 ASN 124 A GLY 125 n 121 GLY 125 A LYS 126 n 122 LYS 126 A PRO 127 n 123 PRO 127 A VAL 128 n 124 VAL 128 A THR 129 n 125 THR 129 A THR 130 n 126 THR 130 A GLY 131 n 127 GLY 131 A VAL 132 n 128 VAL 132 A SER 133 n 129 SER 133 A GLU 134 n 130 GLU 134 A THR 135 n 131 THR 135 A VAL 136 n 132 VAL 136 A PHE 137 n 133 PHE 137 A LEU 138 n 134 LEU 138 A PRO 139 n 135 PRO 139 A ARG 140 n 136 ARG 140 A GLU 141 n 137 GLU 141 A ASP 142 n 138 ASP 142 A HIS 143 n 139 HIS 143 A LEU 144 n 140 LEU 144 A PHE 145 n 141 PHE 145 A ARG 146 n 142 ARG 146 A LYS 147 n 143 LYS 147 A PHE 148 n 144 PHE 148 A HIS 149 n 145 HIS 149 A TYR 150 n 146 TYR 150 A LEU 151 n 147 LEU 151 A PRO 152 n 148 PRO 152 A PHE 153 n 149 PHE 153 A LEU 154 n 150 LEU 154 A PRO 155 n 151 PRO 155 A SER 156 n 152 SER 156 A THR 157 n 153 THR 157 A GLU 158 n 154 GLU 158 A ASP 159 n 155 ASP 159 A VAL 160 n 156 VAL 160 A TYR 161 n 157 TYR 161 A ASP 162 n 158 ASP 162 A CYS 163 n 159 CYS 163 A ARG 164 n 160 ARG 164 A VAL 165 n 161 VAL 165 A GLU 166 n 162 GLU 166 A HIS 167 n 163 HIS 167 A TRP 168 n 164 TRP 168 A GLY 169 n 165 GLY 169 A LEU 170 n 166 LEU 170 A ASP 171 n 167 ASP 171 A GLU 172 n 168 GLU 172 A PRO 173 n 169 PRO 173 A LEU 174 n 170 LEU 174 A LEU 175 n 171 LEU 175 A LYS 176 n 172 LYS 176 A HIS 177 n 173 HIS 177 A TRP 178 n 174 TRP 178 A GLU 179 n 175 GLU 179 A PHE 180 n 176 PHE 180 A PRO 5 n 1 PRO 5 B ARG 6 n 2 ARG 6 B PHE 7 n 3 PHE 7 B LEU 8 n 4 LEU 8 B GLU 9 n 5 GLU 9 B TYR 10 n 6 TYR 10 B SER 11 n 7 SER 11 B THR 12 n 8 THR 12 B SER 13 n 9 SER 13 B GLU 14 n 10 GLU 14 B CYS 15 n 11 CYS 15 B HIS 16 n 12 HIS 16 B PHE 17 n 13 PHE 17 B PHE 18 n 14 PHE 18 B ASN 19 n 15 ASN 19 B GLY 20 n 16 GLY 20 B THR 21 n 17 THR 21 B GLU 22 n 18 GLU 22 B ARG 23 n 19 ARG 23 B VAL 24 n 20 VAL 24 B ARG 25 n 21 ARG 25 B TYR 26 n 22 TYR 26 B LEU 27 n 23 LEU 27 B ASP 28 n 24 ASP 28 B ARG 29 n 25 ARG 29 B TYR 30 n 26 TYR 30 B PHE 31 n 27 PHE 31 B HIS 32 n 28 HIS 32 B ASN 33 n 29 ASN 33 B GLN 34 n 30 GLN 34 B GLU 35 n 31 GLU 35 B GLU 36 n 32 GLU 36 B ASN 37 n 33 ASN 37 B VAL 38 n 34 VAL 38 B ARG 39 n 35 ARG 39 B PHE 40 n 36 PHE 40 B ASP 41 n 37 ASP 41 B SER 42 n 38 SER 42 B ASP 43 n 39 ASP 43 B VAL 44 n 40 VAL 44 B GLY 45 n 41 GLY 45 B GLU 46 n 42 GLU 46 B PHE 47 n 43 PHE 47 B ARG 48 n 44 ARG 48 B ALA 49 n 45 ALA 49 B VAL 50 n 46 VAL 50 B THR 51 n 47 THR 51 B GLU 52 n 48 GLU 52 B LEU 53 n 49 LEU 53 B GLY 54 n 50 GLY 54 B ARG 55 n 51 ARG 55 B PRO 56 n 52 PRO 56 B ASP 57 n 53 ASP 57 B ALA 58 n 54 ALA 58 B GLU 59 n 55 GLU 59 B TYR 60 n 56 TYR 60 B TRP 61 n 57 TRP 61 B ASN 62 n 58 ASN 62 B SER 63 n 59 SER 63 B GLN 64 n 60 GLN 64 B LYS 65 n 61 LYS 65 B ASP 66 n 62 ASP 66 B LEU 67 n 63 LEU 67 B LEU 68 n 64 LEU 68 B GLU 69 n 65 GLU 69 B GLN 70 n 66 GLN 70 B LYS 71 n 67 LYS 71 B ARG 72 n 68 ARG 72 B GLY 73 n 69 GLY 73 B ARG 74 n 70 ARG 74 B VAL 75 n 71 VAL 75 B ASP 76 n 72 ASP 76 B ASN 77 n 73 ASN 77 B TYR 78 n 74 TYR 78 B CYS 79 n 75 CYS 79 B ARG 80 n 76 ARG 80 B HIS 81 n 77 HIS 81 B ASN 82 n 78 ASN 82 B TYR 83 n 79 TYR 83 B GLY 84 n 80 GLY 84 B VAL 85 n 81 VAL 85 B VAL 86 n 82 VAL 86 B GLU 87 n 83 GLU 87 B SER 88 n 84 SER 88 B PHE 89 n 85 PHE 89 B THR 90 n 86 THR 90 B VAL 91 n 87 VAL 91 B GLN 92 n 88 GLN 92 B ARG 93 n 89 ARG 93 B ARG 94 n 90 ARG 94 B VAL 95 n 91 VAL 95 B HIS 96 n 92 HIS 96 B PRO 97 n 93 PRO 97 B LYS 98 n 94 LYS 98 B VAL 99 n 95 VAL 99 B THR 100 n 96 THR 100 B VAL 101 n 97 VAL 101 B TYR 102 n 98 TYR 102 B PRO 103 n 99 PRO 103 B SER 104 n 100 SER 104 B LYS 105 n 101 LYS 105 B THR 106 n 102 THR 106 B GLN 107 n 103 GLN 107 B PRO 108 n 104 PRO 108 B LEU 109 n 105 LEU 109 B GLN 110 n 106 GLN 110 B HIS 111 n 107 HIS 111 B HIS 112 n 108 HIS 112 B ASN 113 n 109 ASN 113 B LEU 114 n 110 LEU 114 B LEU 115 n 111 LEU 115 B VAL 116 n 112 VAL 116 B CYS 117 n 113 CYS 117 B SER 118 n 114 SER 118 B VAL 119 n 115 VAL 119 B SER 120 n 116 SER 120 B GLY 121 n 117 GLY 121 B PHE 122 n 118 PHE 122 B TYR 123 n 119 TYR 123 B PRO 124 n 120 PRO 124 B GLY 125 n 121 GLY 125 B SER 126 n 122 SER 126 B ILE 127 n 123 ILE 127 B GLU 128 n 124 GLU 128 B VAL 129 n 125 VAL 129 B ARG 130 n 126 ARG 130 B TRP 131 n 127 TRP 131 B PHE 132 n 128 PHE 132 B ARG 133 n 129 ARG 133 B ASN 134 n 130 ASN 134 B GLY 135 n 131 GLY 135 B GLN 136 n 132 GLN 136 B GLU 137 n 133 GLU 137 B GLU 138 n 134 GLU 138 B LYS 139 n 135 LYS 139 B THR 140 n 136 THR 140 B GLY 141 n 137 GLY 141 B VAL 142 n 138 VAL 142 B VAL 143 n 139 VAL 143 B SER 144 n 140 SER 144 B THR 145 n 141 THR 145 B GLY 146 n 142 GLY 146 B LEU 147 n 143 LEU 147 B ILE 148 n 144 ILE 148 B HIS 149 n 145 HIS 149 B ASN 150 n 146 ASN 150 B GLY 151 n 147 GLY 151 B ASP 152 n 148 ASP 152 B TRP 153 n 149 TRP 153 B THR 154 n 150 THR 154 B PHE 155 n 151 PHE 155 B GLN 156 n 152 GLN 156 B THR 157 n 153 THR 157 B LEU 158 n 154 LEU 158 B VAL 159 n 155 VAL 159 B MET 160 n 156 MET 160 B LEU 161 n 157 LEU 161 B GLU 162 n 158 GLU 162 B THR 163 n 159 THR 163 B VAL 164 n 160 VAL 164 B PRO 165 n 161 PRO 165 B ARG 166 n 162 ARG 166 B SER 167 n 163 SER 167 B GLY 168 n 164 GLY 168 B GLU 169 n 165 GLU 169 B VAL 170 n 166 VAL 170 B TYR 171 n 167 TYR 171 B THR 172 n 168 THR 172 B CYS 173 n 169 CYS 173 B GLN 174 n 170 GLN 174 B VAL 175 n 171 VAL 175 B GLU 176 n 172 GLU 176 B HIS 177 n 173 HIS 177 B PRO 178 n 174 PRO 178 B SER 179 n 175 SER 179 B VAL 180 n 176 VAL 180 B THR 181 n 177 THR 181 B SER 182 n 178 SER 182 B PRO 183 n 179 PRO 183 B LEU 184 n 180 LEU 184 B THR 185 n 181 THR 185 B VAL 186 n 182 VAL 186 B GLU 187 n 183 GLU 187 B TRP 188 n 184 TRP 188 B ARG 189 n 185 ARG 189 B ALA 190 n 186 ALA 190 B ARG 191 n 187 ARG 191 B PRO 87 n 1 PRO 87 C VAL 88 n 2 VAL 88 C SER 89 n 3 SER 89 C LYS 90 n 4 LYS 90 C MET 91 n 5 MET 91 C ARG 92 n 6 ARG 92 C MET 93 n 7 MET 93 C ALA 94 n 8 ALA 94 C THR 95 n 9 THR 95 C PRO 96 n 10 PRO 96 C LEU 97 n 11 LEU 97 C LEU 98 n 12 LEU 98 C MET 99 n 13 MET 99 C GLN 100 n 14 GLN 100 C ALA 101 n 15 ALA 101 C author_and_software_defined_assembly PISA 3 trimeric software_defined_assembly PISA 6 hexameric 7340 -42 17990 17000 -85 33650 A ASN 78 GLYCOSYLATION SITE A ASN 74 ASN A ASN 118 GLYCOSYLATION SITE A ASN 114 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 0.5000000000 0.8660254038 0.0000000000 0.8660254038 -0.5000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 6_555 x,x-y,-z crystal symmetry operation 0.0000000000 0.0000000000 0.0000000000 A O ILE 8 A O ILE 4 A N ASP 25 A N ASP 21 A O PHE 24 A O PHE 20 A N PHE 32 A N PHE 28 A O HIS 33 A O HIS 29 A N VAL 42 A N VAL 38 A O THR 90 A O THR 86 A N PHE 108 A N PHE 104 A O ASN 103 A O ASN 99 A N PHE 153 A N PHE 149 A O TYR 150 A O TYR 146 A N SER 133 A N SER 129 A O ASN 118 A O ASN 114 A N GLU 166 A N GLU 162 A O TYR 161 A O TYR 157 A N TRP 178 A N TRP 174 B O TYR 10 B O TYR 6 B N PHE 31 B N PHE 27 B O ASP 28 B O ASP 24 B N PHE 40 B N PHE 36 B O ARG 39 B O ARG 35 B N ARG 48 B N ARG 44 B O LYS 98 B O LYS 94 B N SER 120 B N SER 116 B O VAL 119 B O VAL 115 B N THR 157 B N THR 153 B O GLU 128 B O GLU 124 B N GLU 176 B N GLU 172 B O TYR 171 B O TYR 167 B N TRP 188 B N TRP 184 1 A CG ARG 123 A CG ARG 119 0 Y 1 A CD ARG 123 A CD ARG 119 0 Y 1 A NE ARG 123 A NE ARG 119 0 Y 1 A CZ ARG 123 A CZ ARG 119 0 Y 1 A NH1 ARG 123 A NH1 ARG 119 0 Y 1 A NH2 ARG 123 A NH2 ARG 119 0 Y 1 B CG ASN 19 B CG ASN 15 0 Y 1 B OD1 ASN 19 B OD1 ASN 15 0 Y 1 B ND2 ASN 19 B ND2 ASN 15 0 Y 1 B CG GLU 22 B CG GLU 18 0 Y 1 B CD GLU 22 B CD GLU 18 0 Y 1 B OE1 GLU 22 B OE1 GLU 18 0 Y 1 B OE2 GLU 22 B OE2 GLU 18 0 Y 1 B CG ARG 23 B CG ARG 19 0 Y 1 B CD ARG 23 B CD ARG 19 0 Y 1 B NE ARG 23 B NE ARG 19 0 Y 1 B CZ ARG 23 B CZ ARG 19 0 Y 1 B NH1 ARG 23 B NH1 ARG 19 0 Y 1 B NH2 ARG 23 B NH2 ARG 19 0 Y 1 B CG LYS 105 B CG LYS 101 0 Y 1 B CD LYS 105 B CD LYS 101 0 Y 1 B CE LYS 105 B CE LYS 101 0 Y 1 B NZ LYS 105 B NZ LYS 101 0 Y 1 B CG GLN 107 B CG GLN 103 0 Y 1 B CD GLN 107 B CD GLN 103 0 Y 1 B OE1 GLN 107 B OE1 GLN 103 0 Y 1 B NE2 GLN 107 B NE2 GLN 103 0 Y 1 B CG LEU 109 B CG LEU 105 0 Y 1 B CD1 LEU 109 B CD1 LEU 105 0 Y 1 B CD2 LEU 109 B CD2 LEU 105 0 Y 1 B CG GLN 110 B CG GLN 106 0 Y 1 B CD GLN 110 B CD GLN 106 0 Y 1 B OE1 GLN 110 B OE1 GLN 106 0 Y 1 B NE2 GLN 110 B NE2 GLN 106 0 Y 1 B CG HIS 111 B CG HIS 107 0 Y 1 B ND1 HIS 111 B ND1 HIS 107 0 Y 1 B CD2 HIS 111 B CD2 HIS 107 0 Y 1 B CE1 HIS 111 B CE1 HIS 107 0 Y 1 B NE2 HIS 111 B NE2 HIS 107 0 Y 1 B CG GLN 136 B CG GLN 132 0 Y 1 B CD GLN 136 B CD GLN 132 0 Y 1 B OE1 GLN 136 B OE1 GLN 132 0 Y 1 B NE2 GLN 136 B NE2 GLN 132 0 Y 1 B CG GLU 138 B CG GLU 134 0 Y 1 B CD GLU 138 B CD GLU 134 0 Y 1 B OE1 GLU 138 B OE1 GLU 134 0 Y 1 B OE2 GLU 138 B OE2 GLU 134 0 Y 1 B CG ARG 166 B CG ARG 162 0 Y 1 B CD ARG 166 B CD ARG 162 0 Y 1 B NE ARG 166 B NE ARG 162 0 Y 1 B CZ ARG 166 B CZ ARG 162 0 Y 1 B NH1 ARG 166 B NH1 ARG 162 0 Y 1 B NH2 ARG 166 B NH2 ARG 162 0 Y 1 B OG SER 167 B OG SER 163 0 Y 1 B CG ARG 189 B CG ARG 185 0 Y 1 B CD ARG 189 B CD ARG 185 0 Y 1 B NE ARG 189 B NE ARG 185 0 Y 1 B CZ ARG 189 B CZ ARG 185 0 Y 1 B NH1 ARG 189 B NH1 ARG 185 0 Y 1 B NH2 ARG 189 B NH2 ARG 185 0 Y 1 B CG ARG 191 B CG ARG 187 0 Y 1 B CD ARG 191 B CD ARG 187 0 Y 1 B NE ARG 191 B NE ARG 187 0 Y 1 B CZ ARG 191 B CZ ARG 187 0 Y 1 B NH1 ARG 191 B NH1 ARG 187 0 Y 1 B NH2 ARG 191 B NH2 ARG 187 0 Y 1 A TYR 150 0.070 SIDE CHAIN 1 B B C N PHE HIS 31 32 1.18 1 -10.04 1.60 122.70 112.66 B B B O C N PHE PHE HIS 31 31 32 Y 1 B B C N PHE HIS 31 32 -0.159 0.023 1.336 1.177 Y 1 B B CD OE2 GLU GLU 87 87 0.083 0.011 1.252 1.335 N 1 A PHE 32 -171.75 -176.31 1 A THR 90 -163.29 116.89 1 A LYS 111 46.38 73.71 1 A THR 130 -66.28 76.22 1 A HIS 143 39.60 43.33 1 A LEU 144 -109.78 -166.23 1 A LYS 147 177.85 133.60 1 A SER 156 -125.40 -164.53 1 A THR 157 -140.14 -2.32 1 A LEU 170 -175.38 102.73 1 A ASP 171 -35.99 -73.12 1 A PRO 173 -60.90 99.39 1 A GLU 179 -170.93 144.41 1 B ASN 19 58.37 70.53 1 B GLU 22 -52.47 -71.62 1 B GLN 34 71.60 -7.37 1 B SER 88 -52.62 -71.83 1 B THR 90 -120.03 -74.71 1 B HIS 112 -61.30 92.20 1 B TYR 123 -175.42 130.30 1 B PRO 124 -64.34 -172.28 1 B ASN 134 49.43 21.48 1 B GLU 138 -60.77 89.09 1 B ASP 152 -99.97 36.13 1 B SER 167 -63.12 67.98 PARHCSDX.PRO TOPHCSDX.PRO PARAM19.SOL TOPH19.SOL PARAM3_MOD.CHO TOPH3.CHO 47.6 -10. -10. 0. -10. 0. 10. RESIDUES 5 - 180 OF THE ALPHA SUBUNIT AND RESIDUES 5 - 191 OF THE BETA SUBUNIT ARE CLEARLY VISIBLE IN 2FO-FC ELECTRON DENSITY MAPS. THREE SMALL BREAKS IN MAIN-CHAIN DENSITY OCCUR IN LOOP REGIONS OF THE BETA 2 DOMAIN (AT BETA 109, 172, AND 189). 0.325 0.009 0.246 0.246 2.75 6.0 1323 13095 10.1 97.9 RANDOM 10000000.00 0.00 1 RESTRAINED THROUGHOUT 0.0 MOLECULAR REPLACEMENT PDB ENTRY 1DLH 0.53 0.39 5.00 0.72 0.61 2.75 6.0 22 3158 28 0 3108 0.015 1.6 24.6 1.31 3.53 3.00 5.98 4.00 5.52 4.00 9.35 6.00 0.444 0.036 0.373 2.86 162 1442 8 10.1 96.7 30.8 2.75 15. 1A6A 14428 -3. 0.071 1 6.7 3.2 96.9 0.314 2.75 3.0 2.3 1 3.0 97.2 data reduction DENZO data reduction ROTAVATA/AGROVATA phasing AMoRE refinement X-PLOR 3.1 data scaling CCP4 (AGROVATA data scaling ROTAVATA THE STRUCTURE OF AN INTERMEDIATE IN CLASS II MHC MATURATION: CLIP BOUND TO HLA-DR3 1 N N 2 N N 3 N N 4 N N 4 N N 5 N N 5 N N 5 N N A GLU 46 A GLU 42 HELX_P A PHE 51 A PHE 47 1 1 6 A ALA 56 A ALA 52 HELX_P A ARG 76 A ARG 72 1 2 21 B GLU 52 B GLU 48 HELX_P B SER 63 B SER 59 5 3 12 B LYS 65 B LYS 61 HELX_P B ASN 77 B ASN 73 1 4 13 B CYS 79 B CYS 75 HELX_P B VAL 86 B VAL 82 1 5 8 disulf 2.029 A CYS 107 A SG CYS 103 1_555 A CYS 163 A SG CYS 159 1_555 disulf 2.032 B CYS 15 B SG CYS 11 1_555 B CYS 79 B SG CYS 75 1_555 disulf 2.054 B CYS 117 B SG CYS 113 1_555 B CYS 173 B SG CYS 169 1_555 covale 1.453 one N-Glycosylation A ASN 78 A ND2 ASN 74 1_555 A NAG 181 D C1 NAG 1_555 covale 1.440 one N-Glycosylation A ASN 118 A ND2 ASN 114 1_555 A NAG 200 E C1 NAG 1_555 COMPLEX (TRANSMEMBRANE/GLYCOPROTEIN) MHC GLYCOPROTEIN, COMPLEX (TRANSMEMBRANE-GLYCOPROTEIN), COMPLEX (TRANSMEMBRANE-GLYCOPROTEIN) complex A THR 113 A THR 109 1 A PRO 114 A PRO 110 -0.11 B TYR 123 B TYR 119 1 B PRO 124 B PRO 120 -0.51 2DRA_HUMAN UNP 1 1 P01903 MAISGVPVLGFFIIAVLMSAQESWAIKEEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFE AQGALANIAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVTWLRNGKPVTTGVSET VFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWEFDAPSPLPETTENVVCALGLTVGLVGIIIGTIFIIK GVRKSNAAERRGPL HB2B_HUMAN UNP 2 1 P01912 MVCLRLPGGSCMAVLTVTLMVLSSPLALAGDTRPRFLEYSTSECHFFNGTERVRYLDRYFHNQEENVRFDSDVGEFRAVT ELGRPDAEYWNSQKDLLEQKRGRVDNYCRHNYGVVESFTVQRRVHPKVTVYPSKTQPLQHHNLLVCSVSGFYPGSIEVRW FRNGQEEKTGVVSTGLIHNGDWTFQTLVMLETVPRSGEVYTCQVEHPSVTSPLTVEWRARSESAQSKMLSGVGGFVLGLL FLGAGLFIYFRNQKGHSGLQPRGFLS HG2A_HUMAN UNP 3 1 P04233 MHRRRSRSCREDQKPVMDDQRDLISNNEQLPMLGRRPGAPESKCSRGALYTGFSILVTLLLAGQATTAYFLYQQQGRLDK LTVTSQNLQLENLRMKLPKPPKPVSKMRMATPLLMQALPMGALPQGPMQNATKYGNMTEDHVMHLLQNADPLKVYPPLKG SFPENLTHLKNTMETIDWKVFESWMHHWLLFEMSRHSLEQKPTDAPPKVLTKCQEEVSHIPAVHPGSFRPKCDENGNYLP LQCYGSIGYCWCVFPNGTEVPNTRSRGHHNCSESLELEDPSSGLGVTKQDLGPVPM 30 205 1A6A 5 180 P01903 A 1 1 176 34 220 1A6A 5 191 P01912 B 2 1 187 103 117 1A6A 87 101 P04233 C 3 1 15 4 4 3 4 3 3 anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel A ILE 7 A ILE 3 A LEU 14 A LEU 10 A SER 19 A SER 15 A PHE 26 A PHE 22 A ASP 29 A ASP 25 A ASP 35 A ASP 31 A GLU 40 A GLU 36 A TRP 43 A TRP 39 A THR 90 A THR 86 A THR 93 A THR 89 A ASN 103 A ASN 99 A ILE 109 A ILE 105 A LYS 147 A LYS 143 A PHE 153 A PHE 149 A VAL 132 A VAL 128 A GLU 134 A GLU 130 A ASN 118 A ASN 114 A ARG 123 A ARG 119 A VAL 160 A VAL 156 A GLU 166 A GLU 162 A LEU 174 A LEU 170 A GLU 179 A GLU 175 B GLU 9 B GLU 5 B PHE 18 B PHE 14 B ARG 23 B ARG 19 B HIS 32 B HIS 28 B GLU 35 B GLU 31 B ASP 41 B ASP 37 B PHE 47 B PHE 43 B ALA 49 B ALA 45 B LYS 98 B LYS 94 B PRO 103 B PRO 99 B LEU 115 B LEU 111 B SER 120 B SER 116 B GLN 156 B GLN 152 B LEU 158 B LEU 154 B ILE 127 B ILE 123 B ARG 133 B ARG 129 B VAL 170 B VAL 166 B HIS 177 B HIS 173 B LEU 184 B LEU 180 B ARG 189 B ARG 185 153 P 32 1 2