data_4IRJ # _model_server_result.job_id ioaAYp5MqKpfCdbt2dxcjQ _model_server_result.datetime_utc '2024-10-12 10:15:04' _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 4irj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":306}' # _entry.id 4IRJ # _exptl.entry_id 4IRJ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 1011.888 _entity.id 7 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description N-[(2S,3S,4R)-1-({6-O-[(4-chlorophenyl)carbamoyl]-alpha-D-galactopyranosyl}oxy)-3,4-dihydroxyoctadecan-2-yl]hexacosanamide _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 4IRJ _cell.length_a 79.283 _cell.length_b 191.862 _cell.length_c 151.598 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4IRJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _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,H,I,J,K _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 7 _struct_asym.id H _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 5 _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 ? 5 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 5 3 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 5 n E NAG 1 E 1 NAG E 511 NAG 5 n E NAG 2 E 2 NAG E 512 NAG 5 n E FUC 3 E 3 FUC E 513 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? disulf ? disulf2 A SG CYS 208 A CYS 208 1_555 A SG CYS 263 A CYS 263 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf3 B SG CYS 25 B CYS 25 1_555 B SG CYS 80 B CYS 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf4 C SG CYS 24 C CYS 23 1_555 C SG CYS 91 C CYS 90 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf5 C SG CYS 138 C CYS 137 1_555 C SG CYS 188 C CYS 187 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? disulf ? disulf6 C SG CYS 163 C CYS 162 1_555 D SG CYS 169 D CYS 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf7 D SG CYS 24 D CYS 23 1_555 D SG CYS 92 D CYS 91 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf8 D SG CYS 143 D CYS 142 1_555 D SG CYS 208 D CYS 207 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? covale ? covale1 A ND2 ASN 20 A ASN 20 1_555 F C1 NAG . A NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale2 A ND2 ASN 42 A ASN 42 1_555 G C1 NAG . A NAG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale3 A ND2 ASN 165 A ASN 165 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale4 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale5 E O6 NAG . E NAG 1 1_555 E C1 FUC . E FUC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? # _chem_comp.formula 'C57 H103 Cl N2 O10' _chem_comp.formula_weight 1011.888 _chem_comp.id 1L9 _chem_comp.mon_nstd_flag . _chem_comp.name N-[(2S,3S,4R)-1-({6-O-[(4-chlorophenyl)carbamoyl]-alpha-D-galactopyranosyl}oxy)-3,4-dihydroxyoctadecan-2-yl]hexacosanamide _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 4IRJ _atom_sites.fract_transf_matrix[1][1] 0.012613 _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] 0.005212 _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] 0.006596 _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 1 301 500 NAG NAG . G 6 NAG A 1 302 501 NAG NAG . H 7 1L9 A 1 306 1 1L9 NP2 . I 8 HOH A 1 401 4 HOH HOH . I 8 HOH A 2 402 5 HOH HOH . I 8 HOH A 3 403 7 HOH HOH . I 8 HOH A 4 404 9 HOH HOH . I 8 HOH A 5 405 10 HOH HOH . I 8 HOH A 6 406 13 HOH HOH . J 8 HOH C 1 301 1 HOH HOH . J 8 HOH C 2 302 8 HOH HOH . J 8 HOH C 3 303 14 HOH HOH . J 8 HOH C 4 304 17 HOH HOH . K 8 HOH D 1 301 11 HOH HOH . K 8 HOH D 2 302 12 HOH HOH . K 8 HOH D 3 303 16 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 C CAZ 1L9 . . . H 7 8.383 16.214 19.091 1 55.44 ? CAZ 1L9 306 A 1 HETATM 2 C CAY 1L9 . . . H 7 7.622 15.502 20.215 1 55.84 ? CAY 1L9 306 A 1 HETATM 3 C CAX 1L9 . . . H 7 8.43 14.31 20.753 1 56.34 ? CAX 1L9 306 A 1 HETATM 4 C CAW 1L9 . . . H 7 8.795 14.573 22.217 1 56.05 ? CAW 1L9 306 A 1 HETATM 5 C CAV 1L9 . . . H 7 7.861 13.785 23.145 1 55.38 ? CAV 1L9 306 A 1 HETATM 6 C CAU 1L9 . . . H 7 7.66 14.558 24.457 1 53.12 ? CAU 1L9 306 A 1 HETATM 7 C CAT 1L9 . . . H 7 6.188 14.952 24.607 1 50.13 ? CAT 1L9 306 A 1 HETATM 8 C CAS 1L9 . . . H 7 6.029 15.915 25.781 1 48.62 ? CAS 1L9 306 A 1 HETATM 9 C CAR 1L9 . . . H 7 4.592 16.433 25.818 1 48.85 ? CAR 1L9 306 A 1 HETATM 10 C CAQ 1L9 . . . H 7 4.582 17.955 25.598 1 49.89 ? CAQ 1L9 306 A 1 HETATM 11 C CAP 1L9 . . . H 7 4.341 18.303 24.122 1 48.4 ? CAP 1L9 306 A 1 HETATM 12 C CAO 1L9 . . . H 7 3.464 19.555 24.018 1 47.04 ? CAO 1L9 306 A 1 HETATM 13 C CAN 1L9 . . . H 7 4.08 20.55 23.03 1 46.93 ? CAN 1L9 306 A 1 HETATM 14 C CAM 1L9 . . . H 7 3.569 20.277 21.612 1 47.5 ? CAM 1L9 306 A 1 HETATM 15 C CAL 1L9 . . . H 7 4.303 21.198 20.625 1 46.57 ? CAL 1L9 306 A 1 HETATM 16 C CAK 1L9 . . . H 7 4.567 20.467 19.298 1 44.46 ? CAK 1L9 306 A 1 HETATM 17 C CAJ 1L9 . . . H 7 5.984 19.887 19.332 1 44.23 ? CAJ 1L9 306 A 1 HETATM 18 C CAI 1L9 . . . H 7 6.76 20.251 18.062 1 42.6 ? CAI 1L9 306 A 1 HETATM 19 C CAH 1L9 . . . H 7 7.855 21.275 18.392 1 40.41 ? CAH 1L9 306 A 1 HETATM 20 C CAG 1L9 . . . H 7 9.222 20.647 18.126 1 39.01 ? CAG 1L9 306 A 1 HETATM 21 C CAF 1L9 . . . H 7 10.233 21.744 17.786 1 37.85 ? CAF 1L9 306 A 1 HETATM 22 C CAE 1L9 . . . H 7 11.014 22.12 19.052 1 38.07 ? CAE 1L9 306 A 1 HETATM 23 C CAD 1L9 . . . H 7 12.144 23.096 18.716 1 37.02 ? CAD 1L9 306 A 1 HETATM 24 C CAC 1L9 . . . H 7 13.19 23.066 19.83 1 36.8 ? CAC 1L9 306 A 1 HETATM 25 C CAB 1L9 . . . H 7 14.318 24.048 19.484 1 38.93 ? CAB 1L9 306 A 1 HETATM 26 C CAA 1L9 . . . H 7 13.93 25.486 19.858 1 39.1 ? CAA 1L9 306 A 1 HETATM 27 O OAA 1L9 . . . H 7 13.469 25.732 20.976 1 38.96 ? OAA 1L9 306 A 1 HETATM 28 N N2 1L9 . . . H 7 14.158 26.41 18.897 1 38.94 ? N2 1L9 306 A 1 HETATM 29 C C2 1L9 . . . H 7 13.811 27.829 19.072 1 40.63 ? C2 1L9 306 A 1 HETATM 30 C C3 1L9 . . . H 7 13.712 28.562 17.724 1 41.6 ? C3 1L9 306 A 1 HETATM 31 O O3 1L9 . . . H 7 13.124 29.841 17.937 1 43.1 ? O3 1L9 306 A 1 HETATM 32 C C4 1L9 . . . H 7 12.917 27.866 16.618 1 42.46 ? C4 1L9 306 A 1 HETATM 33 O O4 1L9 . . . H 7 13.052 28.687 15.458 1 42.55 ? O4 1L9 306 A 1 HETATM 34 C C5 1L9 . . . H 7 11.422 27.7 16.964 1 43.56 ? C5 1L9 306 A 1 HETATM 35 C C6 1L9 . . . H 7 10.603 27.354 15.702 1 43.99 ? C6 1L9 306 A 1 HETATM 36 C C7 1L9 . . . H 7 10.691 25.855 15.37 1 43.67 ? C7 1L9 306 A 1 HETATM 37 C C8 1L9 . . . H 7 9.412 25.398 14.649 1 45.62 ? C8 1L9 306 A 1 HETATM 38 C C9 1L9 . . . H 7 9.471 25.793 13.159 1 45.64 ? C9 1L9 306 A 1 HETATM 39 C C10 1L9 . . . H 7 8.186 25.384 12.417 1 43.52 ? C10 1L9 306 A 1 HETATM 40 C C11 1L9 . . . H 7 8.233 25.918 10.979 1 40.14 ? C11 1L9 306 A 1 HETATM 41 C C12 1L9 . . . H 7 6.974 26.729 10.685 1 39.79 ? C12 1L9 306 A 1 HETATM 42 C C13 1L9 . . . H 7 7.001 27.279 9.246 1 41.13 ? C13 1L9 306 A 1 HETATM 43 C C14 1L9 . . . H 7 7.065 28.82 9.281 1 41.64 ? C14 1L9 306 A 1 HETATM 44 C C15 1L9 . . . H 7 5.955 29.463 8.438 1 40.56 ? C15 1L9 306 A 1 HETATM 45 C C16 1L9 . . . H 7 6.345 30.921 8.121 1 41.51 ? C16 1L9 306 A 1 HETATM 46 C C17 1L9 . . . H 7 5.118 31.847 8.231 1 43.39 ? C17 1L9 306 A 1 HETATM 47 C C18 1L9 . . . H 7 5.413 33.236 7.642 1 41.93 ? C18 1L9 306 A 1 HETATM 48 C C1 1L9 . . . H 7 14.885 28.545 19.908 1 43.51 ? C1 1L9 306 A 1 HETATM 49 O O1A 1L9 . . . H 7 16.099 28.681 19.137 1 47.16 ? O1A 1L9 306 A 1 HETATM 50 C C1A 1L9 . . . H 7 17.252 29.088 19.903 1 47.44 ? C1A 1L9 306 A 1 HETATM 51 O O6A 1L9 . . . H 7 17.426 28.338 21.138 1 48.52 ? O6A 1L9 306 A 1 HETATM 52 C C2A 1L9 . . . H 7 18.501 28.942 19.027 1 49.91 ? C2A 1L9 306 A 1 HETATM 53 O O2A 1L9 . . . H 7 18.253 29.493 17.72 1 49.22 ? O2A 1L9 306 A 1 HETATM 54 C C3A 1L9 . . . H 7 18.905 27.463 18.873 1 51.29 ? C3A 1L9 306 A 1 HETATM 55 O O3A 1L9 . . . H 7 20.167 27.388 18.2 1 52.69 ? O3A 1L9 306 A 1 HETATM 56 C C4A 1L9 . . . H 7 18.991 26.759 20.227 1 53.45 ? C4A 1L9 306 A 1 HETATM 57 O O4A 1L9 . . . H 7 20.051 27.341 21.017 1 55.02 ? O4A 1L9 306 A 1 HETATM 58 C C5M 1L9 . . . H 7 17.636 26.943 20.908 1 53.57 ? C5M 1L9 306 A 1 HETATM 59 C C6A 1L9 . . . H 7 17.469 26.135 22.206 1 60.95 ? C6A 1L9 306 A 1 HETATM 60 O OAZ 1L9 . . . H 7 18.702 25.999 22.919 1 73.01 ? OAZ 1L9 306 A 1 HETATM 61 C CCI 1L9 . . . H 7 18.878 24.741 23.431 1 82.33 ? CCI 1L9 306 A 1 HETATM 62 O OCK 1L9 . . . H 7 19.703 24.576 24.329 1 81.8 ? OCK 1L9 306 A 1 HETATM 63 N NCJ 1L9 . . . H 7 18.166 23.689 22.958 1 91.52 ? NCJ 1L9 306 A 1 HETATM 64 C CCU 1L9 . . . H 7 18.379 22.463 23.468 1 100.79 ? CCU 1L9 306 A 1 HETATM 65 C CCL 1L9 . . . H 7 17.613 21.982 24.542 1 103.13 ? CCL 1L9 306 A 1 HETATM 66 C CCQ 1L9 . . . H 7 17.846 20.701 25.054 1 104.98 ? CCQ 1L9 306 A 1 HETATM 67 C CCR 1L9 . . . H 7 18.843 19.9 24.484 1 109.11 ? CCR 1L9 306 A 1 HETATM 68 CL CL1 1L9 . . . H 7 19.152 18.31 25.099 1 117.36 ? CL1 1L9 306 A 1 HETATM 69 C CCS 1L9 . . . H 7 19.605 20.37 23.411 1 104.78 ? CCS 1L9 306 A 1 HETATM 70 C CCT 1L9 . . . H 7 19.371 21.648 22.905 1 101.49 ? CCT 1L9 306 A 1 # _model_server_stats.io_time_ms 29 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 271 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 70 #