data_3SDD # _model_server_result.job_id yLm4DYG23ztS1eFcbbRf-Q _model_server_result.datetime_utc '2024-10-12 09:21:52' _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 3sdd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":307}' # _entry.id 3SDD # _exptl.entry_id 3SDD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 946.341 _entity.id 7 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description N-[(2S,3R,4E)-1-{[4-O-(beta-D-galactopyranosyl)-beta-D-glucopyranosyl]oxy}-3-hydroxyoctadec-4-en-2-yl]docosanamide _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 3SDD _cell.length_a 94.469 _cell.length_b 94.469 _cell.length_c 291.063 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3SDD _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 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,H,I,J,K,L _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 # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 5 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order 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 A 305 NAG 5 n E NAG 2 E 2 NAG A 306 NAG # 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf2 A SG CYS 208 A CYS 208 1_555 A SG CYS 263 A CYS 263 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf3 B SG CYS 25 B CYS 25 1_555 B SG CYS 80 B CYS 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf4 C SG CYS 22 C CYS 22 1_555 C SG CYS 89 C CYS 90 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf5 C SG CYS 136 C CYS 139 1_555 C SG CYS 186 C CYS 189 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf6 C SG CYS 161 C CYS 164 1_555 D SG CYS 172 D CYS 174 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf7 D SG CYS 25 D CYS 23 1_555 D SG CYS 93 D CYS 91 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf8 D SG CYS 146 D CYS 148 1_555 D SG CYS 211 D CYS 213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? covale ? covale1 A ND2 ASN 20 A ASN 20 1_555 G C1 NAG . A NAG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale2 A ND2 ASN 42 A ASN 42 1_555 F C1 NAG . A NAG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale3 A ND2 ASN 165 A ASN 165 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale4 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.457 ? # _chem_comp.formula 'C52 H99 N O13' _chem_comp.formula_weight 946.341 _chem_comp.id 3GD _chem_comp.mon_nstd_flag . _chem_comp.name N-[(2S,3R,4E)-1-{[4-O-(beta-D-galactopyranosyl)-beta-D-glucopyranosyl]oxy}-3-hydroxyoctadec-4-en-2-yl]docosanamide _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 3SDD _atom_sites.fract_transf_matrix[1][1] 0.010585 _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] 0.010585 _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] 0.003436 _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 1 304 304 NAG NAG . G 6 NAG A 1 303 303 NAG NAG . H 7 3GD A 1 307 1 3GD 3GD . I 8 HOH A 1 308 1 HOH HOH . I 8 HOH A 2 309 5 HOH HOH . I 8 HOH A 3 310 6 HOH HOH . I 8 HOH A 4 311 7 HOH HOH . I 8 HOH A 5 312 8 HOH HOH . I 8 HOH A 6 313 9 HOH HOH . I 8 HOH A 7 314 10 HOH HOH . I 8 HOH A 8 315 11 HOH HOH . I 8 HOH A 9 316 13 HOH HOH . I 8 HOH A 10 317 26 HOH HOH . I 8 HOH A 11 318 45 HOH HOH . I 8 HOH A 12 319 46 HOH HOH . I 8 HOH A 13 320 48 HOH HOH . I 8 HOH A 14 321 49 HOH HOH . J 8 HOH B 1 100 14 HOH HOH . J 8 HOH B 2 101 16 HOH HOH . K 8 HOH C 1 211 17 HOH HOH . K 8 HOH C 2 212 18 HOH HOH . K 8 HOH C 3 213 25 HOH HOH . L 8 HOH D 1 248 3 HOH HOH . L 8 HOH D 2 249 12 HOH HOH . L 8 HOH D 3 250 19 HOH HOH . L 8 HOH D 4 251 20 HOH HOH . L 8 HOH D 5 252 22 HOH HOH . L 8 HOH D 6 253 36 HOH HOH . L 8 HOH D 7 254 39 HOH HOH . L 8 HOH D 8 255 40 HOH HOH . L 8 HOH D 9 256 41 HOH HOH . L 8 HOH D 10 257 44 HOH HOH . L 8 HOH D 11 258 47 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 C 3GD . . . H 7 -4.75 -94.73 -52.772 1 72.24 ? C 3GD 307 A 1 HETATM 2 N N 3GD . . . H 7 -2.768 -94.865 -54.254 1 72.18 ? N 3GD 307 A 1 HETATM 3 O O 3GD . . . H 7 -5.158 -94.121 -51.428 1 72.23 ? O 3GD 307 A 1 HETATM 4 O O1 3GD . . . H 7 0.918 -91.984 -63.409 1 90.68 ? O1 3GD 307 A 1 HETATM 5 C CA 3GD . . . H 7 -3.604 -93.957 -53.447 1 73.14 ? CA 3GD 307 A 1 HETATM 6 C CB 3GD . . . H 7 -4.189 -92.86 -54.353 1 75.51 ? CB 3GD 307 A 1 HETATM 7 C CAL 3GD . . . H 7 0.361 -90.995 -60.132 1 89.25 ? CAL 3GD 307 A 1 HETATM 8 C CAM 3GD . . . H 7 1.708 -91.641 -60.526 1 90 ? CAM 3GD 307 A 1 HETATM 9 C CAN 3GD . . . H 7 2.36 -90.946 -61.74 1 90.41 ? CAN 3GD 307 A 1 HETATM 10 C CAO 3GD . . . H 7 1.348 -90.718 -62.868 1 90.9 ? CAO 3GD 307 A 1 HETATM 11 C CAP 3GD . . . H 7 0.158 -89.942 -62.305 1 91.02 ? CAP 3GD 307 A 1 HETATM 12 C CAQ 3GD . . . H 7 -0.835 -89.596 -63.42 1 91.76 ? CAQ 3GD 307 A 1 HETATM 13 O OAR 3GD . . . H 7 2.614 -91.577 -59.415 1 90.02 ? OAR 3GD 307 A 1 HETATM 14 O OAS 3GD . . . H 7 3.442 -91.757 -62.226 1 90.71 ? OAS 3GD 307 A 1 HETATM 15 O OAU 3GD . . . H 7 -0.482 -90.738 -61.285 1 90.28 ? OAU 3GD 307 A 1 HETATM 16 O OAV 3GD . . . H 7 -1.969 -88.927 -62.86 1 92.38 ? OAV 3GD 307 A 1 HETATM 17 C CAW 3GD . . . H 7 -2.994 -90.788 -56.797 1 82.23 ? CAW 3GD 307 A 1 HETATM 18 C CAX 3GD . . . H 7 -2.369 -91.072 -58.173 1 83.61 ? CAX 3GD 307 A 1 HETATM 19 C CAY 3GD . . . H 7 -0.849 -91.359 -58.072 1 84.54 ? CAY 3GD 307 A 1 HETATM 20 C CAZ 3GD . . . H 7 -0.564 -92.366 -56.933 1 83.6 ? CAZ 3GD 307 A 1 HETATM 21 C CBA 3GD . . . H 7 0.945 -92.566 -56.729 1 83.87 ? CBA 3GD 307 A 1 HETATM 22 C CBB 3GD . . . H 7 -2.61 -91.918 -55.844 1 80.97 ? CBB 3GD 307 A 1 HETATM 23 O OBC 3GD . . . H 7 -3.253 -91.786 -54.554 1 78.74 ? OBC 3GD 307 A 1 HETATM 24 O OBD 3GD . . . H 7 -4.421 -90.714 -56.92 1 81.23 ? OBD 3GD 307 A 1 HETATM 25 O OBE 3GD . . . H 7 -2.596 -89.946 -59.036 1 83.6 ? OBE 3GD 307 A 1 HETATM 26 O OBF 3GD . . . H 7 -0.381 -91.919 -59.315 1 87.06 ? OBF 3GD 307 A 1 HETATM 27 O OBG 3GD . . . H 7 -1.176 -91.93 -55.695 1 82.31 ? OBG 3GD 307 A 1 HETATM 28 O OBH 3GD . . . H 7 1.499 -91.458 -56.014 1 84.06 ? OBH 3GD 307 A 1 HETATM 29 C CBI 3GD . . . H 7 -15.214 -98.858 -46.218 0.5 60.82 ? CBI 3GD 307 A 1 HETATM 30 C CBJ 3GD . . . H 7 -15.268 -99.818 -47.408 0.5 60.97 ? CBJ 3GD 307 A 1 HETATM 31 C CBK 3GD . . . H 7 -13.848 -100.237 -47.791 0.5 61.08 ? CBK 3GD 307 A 1 HETATM 32 C CBL 3GD . . . H 7 -13.819 -101.736 -48.096 0.5 61.29 ? CBL 3GD 307 A 1 HETATM 33 C CBM 3GD . . . H 7 -12.401 -102.272 -47.888 0.5 61.35 ? CBM 3GD 307 A 1 HETATM 34 C CBN 3GD . . . H 7 -11.795 -102.649 -49.241 0.5 61.64 ? CBN 3GD 307 A 1 HETATM 35 C CBO 3GD . . . H 7 -11.093 -101.431 -49.845 0.5 61.93 ? CBO 3GD 307 A 1 HETATM 36 C CBP 3GD . . . H 7 -11.147 -101.518 -51.372 0.5 62.38 ? CBP 3GD 307 A 1 HETATM 37 C CBQ 3GD . . . H 7 -9.725 -101.603 -51.93 0.5 63.02 ? CBQ 3GD 307 A 1 HETATM 38 C CBR 3GD . . . H 7 -8.749 -100.965 -50.94 0.5 64.02 ? CBR 3GD 307 A 1 HETATM 39 C CBS 3GD . . . H 7 -7.532 -100.426 -51.696 0.5 65.1 ? CBS 3GD 307 A 1 HETATM 40 C CBT 3GD . . . H 7 -7.344 -98.946 -51.363 0.5 66.62 ? CBT 3GD 307 A 1 HETATM 41 C CBU 3GD . . . H 7 -6.123 -98.393 -52.103 0.5 68.1 ? CBU 3GD 307 A 1 HETATM 42 C CBV 3GD . . . H 7 -6.019 -96.868 -52.086 1 69.52 ? CBV 3GD 307 A 1 HETATM 43 C CBW 3GD . . . H 7 -4.812 -96.264 -52.812 1 70.99 ? CBW 3GD 307 A 1 HETATM 44 C CCC 3GD . . . H 7 -1.424 -94.861 -54.207 1 71.14 ? CCC 3GD 307 A 1 HETATM 45 O OCD 3GD . . . H 7 -0.751 -94.112 -53.498 1 71.26 ? OCD 3GD 307 A 1 HETATM 46 C CCE 3GD . . . H 7 -0.751 -95.876 -55.137 1 70.05 ? CCE 3GD 307 A 1 HETATM 47 C CCF 3GD . . . H 7 0.003 -96.921 -54.312 1 68.8 ? CCF 3GD 307 A 1 HETATM 48 C CCG 3GD . . . H 7 -0.89 -98.144 -54.104 0.5 67.55 ? CCG 3GD 307 A 1 HETATM 49 C CCH 3GD . . . H 7 -0.05 -99.296 -53.555 0.5 66.45 ? CCH 3GD 307 A 1 HETATM 50 C CCI 3GD . . . H 7 -0.979 -100.416 -53.086 0.5 65.52 ? CCI 3GD 307 A 1 HETATM 51 C CCJ 3GD . . . H 7 -0.413 -101.04 -51.812 0.5 64.64 ? CCJ 3GD 307 A 1 HETATM 52 C CCK 3GD . . . H 7 -0.555 -102.559 -51.723 0.5 64.05 ? CCK 3GD 307 A 1 HETATM 53 C CCL 3GD . . . H 7 0.012 -103.176 -50.446 0.5 63.73 ? CCL 3GD 307 A 1 HETATM 54 C CCM 3GD . . . H 7 0.627 -102.173 -49.472 0.5 63.53 ? CCM 3GD 307 A 1 HETATM 55 C CCN 3GD . . . H 7 1.201 -102.782 -48.193 1 63.35 ? CCN 3GD 307 A 1 HETATM 56 C CCO 3GD . . . H 7 2.721 -102.632 -48.207 1 62.95 ? CCO 3GD 307 A 1 HETATM 57 C CCP 3GD . . . H 7 3.213 -102.25 -46.809 1 62.79 ? CCP 3GD 307 A 1 HETATM 58 C CCQ 3GD . . . H 7 4.614 -101.638 -46.904 1 62.69 ? CCQ 3GD 307 A 1 HETATM 59 C CCR 3GD . . . H 7 5.667 -102.748 -46.813 1 62.56 ? CCR 3GD 307 A 1 HETATM 60 C CCS 3GD . . . H 7 7.056 -102.182 -47.124 1 62.4 ? CCS 3GD 307 A 1 HETATM 61 C CCT 3GD . . . H 7 7.43 -102.513 -48.571 1 62.34 ? CCT 3GD 307 A 1 HETATM 62 C CCU 3GD . . . H 7 8.67 -103.412 -48.609 1 62.09 ? CCU 3GD 307 A 1 HETATM 63 C CCV 3GD . . . H 7 9.42 -103.2 -49.928 1 62.37 ? CCV 3GD 307 A 1 HETATM 64 C CCW 3GD . . . H 7 8.878 -104.152 -51.001 1 62.78 ? CCW 3GD 307 A 1 HETATM 65 C CCX 3GD . . . H 7 8.91 -103.458 -52.364 1 62.8 ? CCX 3GD 307 A 1 HETATM 66 C CCY 3GD . . . H 7 7.837 -104.063 -53.272 1 63 ? CCY 3GD 307 A 1 # _model_server_stats.io_time_ms 61 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 323 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 66 #