data_1INY # _model_server_result.job_id -g2mVqdED1i-nKKyvdAj8Q _model_server_result.datetime_utc '2024-11-28 23:22:05' _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 1iny # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":500}' # _entry.id 1INY # _exptl.entry_id 1INY _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 329.241 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (1R)-4-acetamido-1,5-anhydro-2,4-dideoxy-1-phosphono-D-glycero-D-galacto-octitol _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 1INY _cell.length_a 184.86 _cell.length_b 184.86 _cell.length_c 184.86 _cell.Z_PDB 48 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1INY _symmetry.cell_setting ? _symmetry.Int_Tables_number 211 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'I 4 3 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 15_555 y,-x,z 0 1 0 -1 0 0 0 0 1 0 0 0 3 'crystal symmetry operation' 16_555 -y,x,z 0 -1 0 1 0 0 0 0 1 0 0 0 4 'crystal symmetry operation' 2_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id F _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type 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 ? 2 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 2 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 2 4 3 MAN BMA C1 O1 . O3 HO3 . sing 4 ? 2 5 4 MAN MAN C1 O1 . O2 HO2 . sing 5 ? 2 6 5 MAN MAN C1 O1 . O2 HO2 . sing 6 ? 2 7 3 MAN BMA 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 2 n B NAG 1 B 1 NAG ? 200 NAG 2 n B NAG 2 B 2 NAG ? 200 NAG 2 n B BMA 3 B 3 BMA ? 200 MAN 2 n B MAN 4 B 4 MAN ? 200 MAN 2 n B MAN 5 B 5 MAN ? 200 MAN 2 n B MAN 6 B 6 MAN ? 200 MAN 2 n B MAN 7 B 7 MAN ? 200 MAN # 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 11 A CYS 92 1_555 A SG CYS 337 A CYS 418 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? disulf ? disulf2 A SG CYS 43 A CYS 124 1_555 A SG CYS 48 A CYS 129 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? disulf ? disulf3 A SG CYS 95 A CYS 176 1_555 A SG CYS 113 A CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf4 A SG CYS 103 A CYS 184 1_555 A SG CYS 150 A CYS 231 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf5 A SG CYS 152 A CYS 233 1_555 A SG CYS 157 A CYS 238 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.01 ? disulf ? disulf6 A SG CYS 198 A CYS 279 1_555 A SG CYS 211 A CYS 292 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf7 A SG CYS 200 A CYS 281 1_555 A SG CYS 209 A CYS 290 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf8 A SG CYS 238 A CYS 319 1_555 A SG CYS 256 A CYS 337 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf9 A SG CYS 341 A CYS 422 1_555 A SG CYS 367 A CYS 448 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? covale ? covale1 A ND2 ASN 5 A ASN 86 1_555 C C1 NAG . A NAG 470 1_555 ? ? ? A ? ? ? ? ? ? ? ? 1.49 ? covale ? covale2 A ND2 ASN 65 A ASN 146 1_555 D C1 NAG . A NAG 471 1_555 ? ? ? A ? ? ? ? ? ? ? ? 1.475 ? covale ? covale3 A ND2 ASN 119 A ASN 200 1_555 B C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.75 ? covale ? covale4 B O4 NAG . B NAG 1 1_555 B C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.564 ? covale ? covale5 B O4 NAG . B NAG 2 1_555 B C1 BMA . B BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.469 ? covale ? covale6 B O3 BMA . B BMA 3 1_555 B C1 MAN . B MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.405 ? covale ? covale7 B O6 BMA . B BMA 3 1_555 B C1 MAN . B MAN 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale8 B O2 MAN . B MAN 4 1_555 B C1 MAN . B MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.422 ? covale ? covale9 B O2 MAN . B MAN 5 1_555 B C1 MAN . B MAN 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.378 ? metalc ? metalc1 A O ASP 213 A ASP 294 1_555 E CA CA . A CA 479 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.477 ? metalc ? metalc2 A O GLY 217 A GLY 298 1_555 E CA CA . A CA 479 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.86 ? metalc ? metalc3 A OD2 ASP 244 A ASP 325 1_555 E CA CA . A CA 479 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.965 ? metalc ? metalc4 A O ASN 266 A ASN 347 1_555 E CA CA . A CA 479 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.784 ? metalc ? metalc5 E CA CA . A CA 479 1_555 G O HOH . A HOH 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.677 ? # _chem_comp.formula 'C10 H20 N O9 P' _chem_comp.formula_weight 329.241 _chem_comp.id EQP _chem_comp.mon_nstd_flag . _chem_comp.name (1R)-4-acetamido-1,5-anhydro-2,4-dideoxy-1-phosphono-D-glycero-D-galacto-octitol _chem_comp.type d-saccharide _chem_comp.pdbx_synonyms '(4-ACETAMIDO-2,4-DIDEOXY-D-GLYCERO-ALPHA-D-GALACTO-1-OCTOPYRANOSYL)PHOSPHONIC ACID' # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag P1 C2 EQP sing 107 n n P1 O1P EQP doub 108 n n P1 O2P EQP sing 109 n n P1 O3P EQP sing 110 n n C2 C3 EQP sing 111 n n C2 O6 EQP sing 112 n n C2 H2 EQP sing 113 n n C3 C4 EQP sing 114 n n C3 H32 EQP sing 115 n n C3 H31 EQP sing 116 n n C4 C5 EQP sing 117 n n C4 O4 EQP sing 118 n n C4 H4 EQP sing 119 n n C5 C6 EQP sing 120 n n C5 N5 EQP sing 121 n n C5 H5 EQP sing 122 n n C6 C7 EQP sing 123 n n C6 O6 EQP sing 124 n n C6 H6 EQP sing 125 n n C7 C8 EQP sing 126 n n C7 O7 EQP sing 127 n n C7 H7 EQP sing 128 n n C8 C9 EQP sing 129 n n C8 O8 EQP sing 130 n n C8 H8 EQP sing 131 n n C9 O9 EQP sing 132 n n C9 H92 EQP sing 133 n n C9 H91 EQP sing 134 n n C10 C11 EQP sing 135 n n C10 N5 EQP sing 136 n n C10 O10 EQP doub 137 n n C11 H111 EQP sing 138 n n C11 H113 EQP sing 139 n n C11 H112 EQP sing 140 n n N5 HN5 EQP sing 141 n n O2P HOP2 EQP sing 142 n n O3P HOP3 EQP sing 143 n n O4 HO4 EQP sing 144 n n O7 HO7 EQP sing 145 n n O8 HO8 EQP sing 146 n n O9 HO9 EQP sing 147 n n # _atom_sites.entry_id 1INY _atom_sites.fract_transf_matrix[1][1] 0.005409 _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] 0.005409 _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] 0.005409 _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 C 3 NAG A 1 470 86 NAG NAG A D 3 NAG A 1 471 146 NAG NAG A E 4 CA A 1 479 470 CA CA . F 5 EQP A 1 500 500 EQP EQP . G 6 HOH A 1 501 501 HOH HOH . G 6 HOH A 2 502 502 HOH HOH . G 6 HOH A 3 503 503 HOH HOH . G 6 HOH A 4 504 504 HOH HOH . G 6 HOH A 5 505 505 HOH HOH . G 6 HOH A 6 506 506 HOH HOH . G 6 HOH A 7 507 507 HOH HOH . G 6 HOH A 8 508 508 HOH HOH . G 6 HOH A 9 509 509 HOH HOH . G 6 HOH A 10 510 510 HOH HOH . G 6 HOH A 11 511 511 HOH HOH . G 6 HOH A 12 512 512 HOH HOH . G 6 HOH A 13 513 513 HOH HOH . G 6 HOH A 14 514 514 HOH HOH . G 6 HOH A 15 515 515 HOH HOH . G 6 HOH A 16 516 516 HOH HOH . G 6 HOH A 17 517 517 HOH HOH . G 6 HOH A 18 518 518 HOH HOH . G 6 HOH A 19 519 519 HOH HOH . G 6 HOH A 20 520 520 HOH HOH . G 6 HOH A 21 521 521 HOH HOH . G 6 HOH A 22 522 522 HOH HOH . G 6 HOH A 23 523 523 HOH HOH . G 6 HOH A 24 524 524 HOH HOH . G 6 HOH A 25 525 525 HOH HOH . G 6 HOH A 26 526 526 HOH HOH . G 6 HOH A 27 527 527 HOH HOH . G 6 HOH A 28 528 528 HOH HOH . G 6 HOH A 29 529 529 HOH HOH . G 6 HOH A 30 530 530 HOH HOH . G 6 HOH A 31 531 531 HOH HOH . G 6 HOH A 32 532 532 HOH HOH . G 6 HOH A 33 533 533 HOH HOH . G 6 HOH A 34 534 534 HOH HOH . G 6 HOH A 35 535 535 HOH HOH . G 6 HOH A 36 536 536 HOH HOH . G 6 HOH A 37 537 537 HOH HOH . G 6 HOH A 38 538 538 HOH HOH . G 6 HOH A 39 539 539 HOH HOH . G 6 HOH A 40 540 540 HOH HOH . G 6 HOH A 41 541 541 HOH HOH . G 6 HOH A 42 542 542 HOH HOH . G 6 HOH A 43 543 543 HOH HOH . G 6 HOH A 44 544 544 HOH HOH . G 6 HOH A 45 545 545 HOH HOH . G 6 HOH A 46 546 546 HOH HOH . G 6 HOH A 47 547 547 HOH HOH . G 6 HOH A 48 548 548 HOH HOH . G 6 HOH A 49 549 549 HOH HOH . G 6 HOH A 50 550 550 HOH HOH . G 6 HOH A 51 551 551 HOH HOH . G 6 HOH A 52 552 552 HOH HOH . G 6 HOH A 53 553 553 HOH HOH . G 6 HOH A 54 554 554 HOH HOH . G 6 HOH A 55 555 555 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 P P1 EQP . . . F 5 24.514 20.57 67.169 1 21.44 ? P1 EQP 500 A 1 HETATM 2 C C2 EQP . . . F 5 25.118 19.476 65.808 0.95 2 ? C2 EQP 500 A 1 HETATM 3 C C3 EQP . . . F 5 24.82 17.991 66.042 0.95 2 ? C3 EQP 500 A 1 HETATM 4 C C4 EQP . . . F 5 25.218 17.175 64.862 0.95 10.01 ? C4 EQP 500 A 1 HETATM 5 C C5 EQP . . . F 5 26.732 17.169 64.777 0.95 2 ? C5 EQP 500 A 1 HETATM 6 C C6 EQP . . . F 5 27.211 18.683 64.67 0.95 5.01 ? C6 EQP 500 A 1 HETATM 7 C C7 EQP . . . F 5 28.715 18.952 64.835 0.95 23.11 ? C7 EQP 500 A 1 HETATM 8 C C8 EQP . . . F 5 28.897 20.447 64.509 0.95 24.53 ? C8 EQP 500 A 1 HETATM 9 C C9 EQP . . . F 5 30.338 20.836 64.947 0.95 34.89 ? C9 EQP 500 A 1 HETATM 10 C C10 EQP . . . F 5 27.953 15.386 63.629 0.95 2 ? C10 EQP 500 A 1 HETATM 11 C C11 EQP . . . F 5 28.223 14.623 62.341 0.95 2 ? C11 EQP 500 A 1 HETATM 12 N N5 EQP . . . F 5 27.059 16.368 63.571 0.77 2 ? N5 EQP 500 A 1 HETATM 13 O O1P EQP . . . F 5 24.491 19.751 68.367 1 2 ? O1P EQP 500 A 1 HETATM 14 O O2P EQP . . . F 5 25.446 21.673 67.354 1 2 ? O2P EQP 500 A 1 HETATM 15 O O3P EQP . . . F 5 23.129 21.079 67.373 1 28.97 ? O3P EQP 500 A 1 HETATM 16 O O4 EQP . . . F 5 24.734 15.909 64.943 0.83 9.51 ? O4 EQP 500 A 1 HETATM 17 O O6 EQP . . . F 5 26.551 19.548 65.704 0.83 16.23 ? O6 EQP 500 A 1 HETATM 18 O O7 EQP . . . F 5 29.066 18.612 66.173 0.83 29.4 ? O7 EQP 500 A 1 HETATM 19 O O8 EQP . . . F 5 28.658 20.652 63.081 0.83 19.84 ? O8 EQP 500 A 1 HETATM 20 O O9 EQP . . . F 5 31.297 20.371 63.998 0.83 18.79 ? O9 EQP 500 A 1 HETATM 21 O O10 EQP . . . F 5 28.532 15.055 64.682 0.83 2 ? O10 EQP 500 A 1 HETATM 22 H H2 EQP . . . F 5 24.758 19.767 64.849 1 0 ? H2 EQP 500 A 1 HETATM 23 H H32 EQP . . . F 5 23.748 17.894 66.256 1 0 ? H32 EQP 500 A 1 HETATM 24 H H31 EQP . . . F 5 25.393 17.701 66.933 1 0 ? H31 EQP 500 A 1 HETATM 25 H H4 EQP . . . F 5 24.81 17.614 63.932 1 0 ? H4 EQP 500 A 1 HETATM 26 H H5 EQP . . . F 5 27.166 16.75 65.705 1 0 ? H5 EQP 500 A 1 HETATM 27 H H6 EQP . . . F 5 26.877 19.059 63.682 1 0 ? H6 EQP 500 A 1 HETATM 28 H H7 EQP . . . F 5 29.329 18.364 64.143 1 0 ? H7 EQP 500 A 1 HETATM 29 H H8 EQP . . . F 5 28.209 21.07 65.118 1 0 ? H8 EQP 500 A 1 HETATM 30 H H92 EQP . . . F 5 30.594 20.473 65.96 1 0 ? H92 EQP 500 A 1 HETATM 31 H H91 EQP . . . F 5 30.374 21.933 65.016 1 0 ? H91 EQP 500 A 1 HETATM 32 H H111 EQP . . . F 5 28.854 15.246 61.689 1 0 ? H111 EQP 500 A 1 HETATM 33 H H113 EQP . . . F 5 27.267 14.392 61.851 1 0 ? H113 EQP 500 A 1 HETATM 34 H H112 EQP . . . F 5 28.755 13.691 62.589 1 0 ? H112 EQP 500 A 1 HETATM 35 H HN5 EQP . . . F 5 26.532 16.504 62.746 1 0 ? HN5 EQP 500 A 1 HETATM 36 H HOP3 EQP . . . F 5 23.087 21.4 68.274 1 0 ? HOP3 EQP 500 A 1 HETATM 37 H HO4 EQP . . . F 5 25.21 15.325 64.333 1 0 ? HO4 EQP 500 A 1 HETATM 38 H HO7 EQP . . . F 5 28.313 18.871 66.745 1 0 ? HO7 EQP 500 A 1 HETATM 39 H HO8 EQP . . . F 5 29.564 20.759 62.749 1 0 ? HO8 EQP 500 A 1 HETATM 40 H HO9 EQP . . . F 5 32.049 20.003 64.472 1 0 ? HO9 EQP 500 A 1 # _model_server_stats.io_time_ms 79 _model_server_stats.parse_time_ms 25 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 466 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 40 #