data_5EFI # _model_server_result.job_id QTNq-RNXH-iAwJX-loaQLQ _model_server_result.datetime_utc '2024-12-01 11:44:21' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 5efi # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":311}' # _entry.id 5EFI # _exptl.entry_id 5EFI _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 22.99 _entity.id 8 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'SODIUM ION' _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 5EFI _cell.length_a 42.19 _cell.length_b 107.85 _cell.length_c 110.34 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5EFI _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # _struct_asym.details ? _struct_asym.entity_id 8 _struct_asym.id H _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 4 oligosaccharide 5 oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 5 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 5 3 2 BMA NAG C1 O1 . O4 HO4 . sing 4 ? 5 4 3 MAN BMA C1 O1 . O3 HO3 . sing 5 ? 5 5 3 MAN BMA C1 O1 . O6 HO6 . sing 6 ? 5 6 1 FUC NAG C1 O1 . O6 HO6 . sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 4 n D NAG 1 D 1 NAG A 521 NAG 4 n D NAG 2 D 2 NAG A 522 NAG 5 n E NAG 1 E 1 NAG A 511 NAG 5 n E NAG 2 E 2 NAG A 512 NAG 5 n E BMA 3 E 3 BMA A 513 BMA 5 n E MAN 4 E 4 MAN A 516 MAN 5 n E MAN 5 E 5 MAN A 514 MAN 5 n E FUC 6 E 6 FUC A 515 FUC # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.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.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order disulf ? disulf1 A SG CYS 104 A CYS 104 1_555 A SG CYS 168 A CYS 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf2 A SG CYS 208 A CYS 208 1_555 A SG CYS 263 A CYS 263 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf3 B SG CYS 25 B CYS 25 1_555 B SG CYS 80 B CYS 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? covale ? covale1 A ND2 ASN 20 A ASN 20 1_555 F C1 NAG . A NAG 309 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale2 A ND2 ASN 42 A ASN 42 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale3 A ND2 ASN 165 A ASN 165 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale4 C NZ LYS 11 C LYS 7 1_555 I C1 PLM . C PLM 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.351 ? covale ? covale5 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale6 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale7 E O6 NAG . E NAG 1 1_555 E C1 FUC . E FUC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale8 E O4 NAG . E NAG 2 1_555 E C1 BMA . E BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale9 E O3 BMA . E BMA 3 1_555 E C1 MAN . E MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale10 E O6 BMA . E BMA 3 1_555 E C1 MAN . E MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? metalc ? metalc1 A O THR 26 A THR 26 1_555 H NA NA . A NA 311 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.862 ? metalc ? metalc2 A O TRP 40 A TRP 40 1_555 H NA NA . A NA 311 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.628 ? # _chem_comp.formula 'Na 1' _chem_comp.formula_weight 22.99 _chem_comp.id NA _chem_comp.mon_nstd_flag . _chem_comp.name 'SODIUM ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 5EFI _atom_sites.fract_transf_matrix[1][1] 0.023702 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009272 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.009063 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code F 6 NAG A 1 309 501 NAG NAG . G 7 CIT A 1 310 1 CIT CIT . H 8 NA A 1 311 1 NA NA . I 9 PLM C 1 101 100 PLM PLM . J 10 OCA C 1 102 1 OCA OCA . K 11 HOH A 1 401 77 HOH HOH . K 11 HOH A 2 402 94 HOH HOH . K 11 HOH A 3 403 195 HOH HOH . K 11 HOH A 4 404 86 HOH HOH . K 11 HOH A 5 405 27 HOH HOH . K 11 HOH A 6 406 55 HOH HOH . K 11 HOH A 7 407 118 HOH HOH . K 11 HOH A 8 408 58 HOH HOH . K 11 HOH A 9 409 190 HOH HOH . K 11 HOH A 10 410 160 HOH HOH . K 11 HOH A 11 411 13 HOH HOH . K 11 HOH A 12 412 22 HOH HOH . K 11 HOH A 13 413 79 HOH HOH . K 11 HOH A 14 414 90 HOH HOH . K 11 HOH A 15 415 106 HOH HOH . K 11 HOH A 16 416 156 HOH HOH . K 11 HOH A 17 417 176 HOH HOH . K 11 HOH A 18 418 115 HOH HOH . K 11 HOH A 19 419 28 HOH HOH . K 11 HOH A 20 420 83 HOH HOH . K 11 HOH A 21 421 135 HOH HOH . K 11 HOH A 22 422 84 HOH HOH . K 11 HOH A 23 423 159 HOH HOH . K 11 HOH A 24 424 66 HOH HOH . K 11 HOH A 25 425 46 HOH HOH . K 11 HOH A 26 426 31 HOH HOH . K 11 HOH A 27 427 69 HOH HOH . K 11 HOH A 28 428 81 HOH HOH . K 11 HOH A 29 429 2 HOH HOH . K 11 HOH A 30 430 89 HOH HOH . K 11 HOH A 31 431 48 HOH HOH . K 11 HOH A 32 432 14 HOH HOH . K 11 HOH A 33 433 142 HOH HOH . K 11 HOH A 34 434 107 HOH HOH . K 11 HOH A 35 435 4 HOH HOH . K 11 HOH A 36 436 21 HOH HOH . K 11 HOH A 37 437 204 HOH HOH . K 11 HOH A 38 438 20 HOH HOH . K 11 HOH A 39 439 30 HOH HOH . K 11 HOH A 40 440 44 HOH HOH . K 11 HOH A 41 441 182 HOH HOH . K 11 HOH A 42 442 62 HOH HOH . K 11 HOH A 43 443 110 HOH HOH . K 11 HOH A 44 444 8 HOH HOH . K 11 HOH A 45 445 140 HOH HOH . K 11 HOH A 46 446 88 HOH HOH . K 11 HOH A 47 447 15 HOH HOH . K 11 HOH A 48 448 112 HOH HOH . K 11 HOH A 49 449 60 HOH HOH . K 11 HOH A 50 450 163 HOH HOH . K 11 HOH A 51 451 114 HOH HOH . K 11 HOH A 52 452 144 HOH HOH . K 11 HOH A 53 453 56 HOH HOH . K 11 HOH A 54 454 70 HOH HOH . K 11 HOH A 55 455 211 HOH HOH . K 11 HOH A 56 456 141 HOH HOH . K 11 HOH A 57 457 139 HOH HOH . K 11 HOH A 58 458 108 HOH HOH . K 11 HOH A 59 459 197 HOH HOH . K 11 HOH A 60 460 19 HOH HOH . K 11 HOH A 61 461 120 HOH HOH . K 11 HOH A 62 462 82 HOH HOH . K 11 HOH A 63 463 162 HOH HOH . K 11 HOH A 64 464 111 HOH HOH . K 11 HOH A 65 465 16 HOH HOH . K 11 HOH A 66 466 51 HOH HOH . K 11 HOH A 67 467 198 HOH HOH . K 11 HOH A 68 468 104 HOH HOH . K 11 HOH A 69 469 10 HOH HOH . K 11 HOH A 70 470 188 HOH HOH . K 11 HOH A 71 471 167 HOH HOH . K 11 HOH A 72 472 5 HOH HOH . K 11 HOH A 73 473 133 HOH HOH . K 11 HOH A 74 474 199 HOH HOH . K 11 HOH A 75 475 200 HOH HOH . K 11 HOH A 76 476 18 HOH HOH . K 11 HOH A 77 477 186 HOH HOH . K 11 HOH A 78 478 23 HOH HOH . K 11 HOH A 79 479 75 HOH HOH . K 11 HOH A 80 480 131 HOH HOH . K 11 HOH A 81 481 193 HOH HOH . K 11 HOH A 82 482 3 HOH HOH . K 11 HOH A 83 483 149 HOH HOH . K 11 HOH A 84 484 34 HOH HOH . K 11 HOH A 85 485 155 HOH HOH . K 11 HOH A 86 486 100 HOH HOH . K 11 HOH A 87 487 129 HOH HOH . K 11 HOH A 88 488 113 HOH HOH . K 11 HOH A 89 489 12 HOH HOH . K 11 HOH A 90 490 61 HOH HOH . K 11 HOH A 91 491 11 HOH HOH . K 11 HOH A 92 492 35 HOH HOH . K 11 HOH A 93 493 1 HOH HOH . K 11 HOH A 94 494 121 HOH HOH . K 11 HOH A 95 495 192 HOH HOH . K 11 HOH A 96 496 189 HOH HOH . K 11 HOH A 97 497 95 HOH HOH . K 11 HOH A 98 498 134 HOH HOH . K 11 HOH A 99 499 54 HOH HOH . K 11 HOH A 100 500 39 HOH HOH . K 11 HOH A 101 501 212 HOH HOH . K 11 HOH A 102 502 147 HOH HOH . K 11 HOH A 103 503 208 HOH HOH . K 11 HOH A 104 504 76 HOH HOH . K 11 HOH A 105 505 209 HOH HOH . K 11 HOH A 106 506 203 HOH HOH . K 11 HOH A 107 507 105 HOH HOH . K 11 HOH A 108 508 130 HOH HOH . K 11 HOH A 109 509 161 HOH HOH . K 11 HOH A 110 510 145 HOH HOH . K 11 HOH A 111 511 191 HOH HOH . K 11 HOH A 112 512 37 HOH HOH . K 11 HOH A 113 513 206 HOH HOH . K 11 HOH A 114 514 17 HOH HOH . K 11 HOH A 115 515 205 HOH HOH . K 11 HOH A 116 516 97 HOH HOH . K 11 HOH A 117 517 29 HOH HOH . K 11 HOH A 118 518 53 HOH HOH . K 11 HOH A 119 519 214 HOH HOH . K 11 HOH A 120 520 42 HOH HOH . K 11 HOH A 121 521 9 HOH HOH . K 11 HOH A 122 522 24 HOH HOH . K 11 HOH A 123 523 36 HOH HOH . K 11 HOH A 124 524 26 HOH HOH . K 11 HOH A 125 525 128 HOH HOH . K 11 HOH A 126 526 213 HOH HOH . K 11 HOH A 127 527 38 HOH HOH . K 11 HOH A 128 528 183 HOH HOH . K 11 HOH A 129 529 25 HOH HOH . L 11 HOH B 1 101 172 HOH HOH . L 11 HOH B 2 102 98 HOH HOH . L 11 HOH B 3 103 71 HOH HOH . L 11 HOH B 4 104 96 HOH HOH . L 11 HOH B 5 105 138 HOH HOH . L 11 HOH B 6 106 93 HOH HOH . L 11 HOH B 7 107 184 HOH HOH . L 11 HOH B 8 108 32 HOH HOH . L 11 HOH B 9 109 47 HOH HOH . L 11 HOH B 10 110 101 HOH HOH . L 11 HOH B 11 111 68 HOH HOH . L 11 HOH B 12 112 194 HOH HOH . L 11 HOH B 13 113 166 HOH HOH . L 11 HOH B 14 114 175 HOH HOH . L 11 HOH B 15 115 173 HOH HOH . L 11 HOH B 16 116 103 HOH HOH . L 11 HOH B 17 117 99 HOH HOH . L 11 HOH B 18 118 119 HOH HOH . L 11 HOH B 19 119 49 HOH HOH . L 11 HOH B 20 120 136 HOH HOH . L 11 HOH B 21 121 102 HOH HOH . L 11 HOH B 22 122 123 HOH HOH . L 11 HOH B 23 123 87 HOH HOH . L 11 HOH B 24 124 78 HOH HOH . L 11 HOH B 25 125 207 HOH HOH . L 11 HOH B 26 126 196 HOH HOH . L 11 HOH B 27 127 45 HOH HOH . L 11 HOH B 28 128 169 HOH HOH . L 11 HOH B 29 129 92 HOH HOH . L 11 HOH B 30 130 170 HOH HOH . L 11 HOH B 31 131 168 HOH HOH . L 11 HOH B 32 132 125 HOH HOH . L 11 HOH B 33 133 177 HOH HOH . L 11 HOH B 34 134 180 HOH HOH . L 11 HOH B 35 135 72 HOH HOH . L 11 HOH B 36 136 64 HOH HOH . L 11 HOH B 37 137 152 HOH HOH . L 11 HOH B 38 138 124 HOH HOH . L 11 HOH B 39 139 157 HOH HOH . L 11 HOH B 40 140 143 HOH HOH . L 11 HOH B 41 141 91 HOH HOH . L 11 HOH B 42 142 43 HOH HOH . L 11 HOH B 43 143 73 HOH HOH . L 11 HOH B 44 144 153 HOH HOH . L 11 HOH B 45 145 126 HOH HOH . L 11 HOH B 46 146 109 HOH HOH . L 11 HOH B 47 147 67 HOH HOH . L 11 HOH B 48 148 50 HOH HOH . L 11 HOH B 49 149 201 HOH HOH . L 11 HOH B 50 150 41 HOH HOH . L 11 HOH B 51 151 40 HOH HOH . L 11 HOH B 52 152 179 HOH HOH . L 11 HOH B 53 153 57 HOH HOH . L 11 HOH B 54 154 151 HOH HOH . L 11 HOH B 55 155 63 HOH HOH . L 11 HOH B 56 156 137 HOH HOH . L 11 HOH B 57 157 116 HOH HOH . L 11 HOH B 58 158 158 HOH HOH . L 11 HOH B 59 159 132 HOH HOH . L 11 HOH B 60 160 178 HOH HOH . L 11 HOH B 61 161 174 HOH HOH . L 11 HOH B 62 162 150 HOH HOH . L 11 HOH B 63 163 210 HOH HOH . L 11 HOH B 64 164 33 HOH HOH . L 11 HOH B 65 165 187 HOH HOH . L 11 HOH B 66 166 6 HOH HOH . L 11 HOH B 67 167 171 HOH HOH . L 11 HOH B 68 168 146 HOH HOH . L 11 HOH B 69 169 164 HOH HOH . L 11 HOH B 70 170 185 HOH HOH . L 11 HOH B 71 171 85 HOH HOH . L 11 HOH B 72 172 165 HOH HOH . L 11 HOH B 73 173 7 HOH HOH . L 11 HOH B 74 174 181 HOH HOH . M 11 HOH C 1 201 202 HOH HOH . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol NA _atom_site.label_atom_id NA _atom_site.label_comp_id NA _atom_site.label_seq_id . _atom_site.label_alt_id . _atom_site.pdbx_PDB_ins_code . _atom_site.label_asym_id H _atom_site.label_entity_id 8 _atom_site.Cartn_x 21.237 _atom_site.Cartn_y 6.847 _atom_site.Cartn_z 38.694 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 45.74 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NA _atom_site.auth_comp_id NA _atom_site.auth_seq_id 311 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 56 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 366 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 1 #