data_8DVL # _model_server_result.job_id GOMvgXraFtA9kbhS4NUrIA _model_server_result.datetime_utc '2024-11-25 23:07:22' _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 8dvl # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":1309}' # _entry.id 8DVL # _exptl.entry_id 8DVL _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 62.068 _entity.id 8 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1,2-ETHANEDIOL _entity.pdbx_number_of_molecules 7 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 96.58 _cell.angle_gamma 90 _cell.entry_id 8DVL _cell.length_a 57.911 _cell.length_b 73.835 _cell.length_c 87.193 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8DVL _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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,N,O,P,Q,R _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 8 K N N ? 8 L N N ? 8 M N N ? 8 N N N ? 8 O N N ? 8 P N N ? 8 Q N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 3 oligosaccharide 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 ? 3 2 1 FUC NAG C1 O1 . O3 HO3 . sing 2 ? 3 3 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 4 ? 4 3 1 FUC NAG C1 O1 . O6 HO6 . sing 5 ? 5 2 1 NAG NAG C1 O1 . O4 HO4 . sing 6 ? 5 3 2 BMA NAG C1 O1 . O4 HO4 . sing 7 ? 5 4 3 MAN BMA C1 O1 . O6 HO6 . sing 8 ? 5 5 4 MAN MAN C1 O1 . O3 HO3 . sing 9 ? 5 6 3 MAN BMA C1 O1 . O3 HO3 . 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 3 n C NAG 1 C 1 NAG A 1249 NAG 3 n C FUC 2 C 2 FUC A 1251 FUC 3 n C NAG 3 C 3 NAG A 1250 NAG 4 n D NAG 1 D 1 NAG A 1252 NAG 4 n D NAG 2 D 2 NAG A 1253 NAG 4 n D FUC 3 D 3 FUC A 1254 FUC 5 n E NAG 1 E 1 NAG A 1255 NAG 5 n E NAG 2 E 2 NAG A 1256 NAG 5 n E BMA 3 E 3 BMA A 1257 BMA 5 n E MAN 4 E 4 MAN A 1259 MAN 5 n E MAN 5 E 5 MAN A 1260 MAN 5 n E MAN 6 E 6 MAN A 1258 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 264 A CYS 893 1_555 A SG CYS 275 A CYS 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf2 A SG CYS 271 A CYS 900 1_555 A SG CYS 285 A CYS 914 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf3 A SG CYS 287 A CYS 916 1_555 A SG CYS 300 A CYS 929 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf4 A SG CYS 578 A CYS 1207 1_555 A SG CYS 589 A CYS 1218 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? disulf ? disulf5 A SG CYS 585 A CYS 1214 1_555 A SG CYS 599 A CYS 1228 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? disulf ? disulf6 A SG CYS 601 A CYS 1230 1_555 A SG CYS 614 A CYS 1243 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf7 B SG CYS 2 B CYS 2 1_555 B SG CYS 13 B CYS 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? covale ? covale1 A ND2 ASN 63 A ASN 692 1_555 F C1 NAG . A NAG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale2 A ND2 ASN 230 A ASN 859 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale3 A ND2 ASN 236 A ASN 865 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale4 A ND2 ASN 297 A ASN 926 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale5 A C THR 402 A THR 1031 1_555 A N OCS 403 A OCS 1032 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale6 A C OCS 403 A OCS 1032 1_555 A N GLU 404 A GLU 1033 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale7 A ND2 ASN 410 A ASN 1039 1_555 G C1 NAG . A NAG 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale8 C O3 NAG . C NAG 1 1_555 C C1 FUC . C FUC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale9 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.426 ? covale ? covale10 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale11 D O6 NAG . D NAG 1 1_555 D C1 FUC . D FUC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale12 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale13 E O4 NAG . E NAG 2 1_555 E C1 BMA . E BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale14 E O6 BMA . E BMA 3 1_555 E C1 MAN . E MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale15 E O3 BMA . E BMA 3 1_555 E C1 MAN . E MAN 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale16 E O3 MAN . E MAN 4 1_555 E C1 MAN . E MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? metalc ? metalc1 A O LEU 209 A LEU 838 1_555 J CA CA . A CA 1305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.076 ? metalc ? metalc2 A O ILE 433 A ILE 1062 1_555 I CA CA . A CA 1304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.192 ? metalc ? metalc3 A O LEU 521 A LEU 1150 1_555 H CA CA . A CA 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.053 ? metalc ? metalc4 A OD1 ASP 561 A ASP 1190 1_555 H CA CA . A CA 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.14 ? metalc ? metalc5 A O ILE 562 A ILE 1191 1_555 H CA CA . A CA 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.665 ? metalc ? metalc6 H CA CA . A CA 1303 1_555 N O2 EDO . A EDO 1309 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.995 ? metalc ? metalc7 H CA CA . A CA 1303 1_555 N O1 EDO . A EDO 1309 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.529 ? metalc ? metalc8 H CA CA . A CA 1303 1_555 R O HOH . A HOH 1412 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.036 ? metalc ? metalc9 I CA CA . A CA 1304 1_555 N O1 EDO . A EDO 1309 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.577 ? metalc ? metalc10 I CA CA . A CA 1304 1_555 R O HOH . A HOH 1412 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.638 ? metalc ? metalc11 J CA CA . A CA 1305 1_555 R O HOH . A HOH 1413 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.576 ? # _chem_comp.formula 'C2 H6 O2' _chem_comp.formula_weight 62.068 _chem_comp.id EDO _chem_comp.mon_nstd_flag . _chem_comp.name 1,2-ETHANEDIOL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'ETHYLENE GLYCOL' # 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 C1 O1 EDO sing 107 n n C1 C2 EDO sing 108 n n C1 H11 EDO sing 109 n n C1 H12 EDO sing 110 n n O1 HO1 EDO sing 111 n n C2 O2 EDO sing 112 n n C2 H21 EDO sing 113 n n C2 H22 EDO sing 114 n n O2 HO2 EDO sing 115 n n # _atom_sites.entry_id 8DVL _atom_sites.fract_transf_matrix[1][1] 0.017268 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001992 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013544 _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] 0.011545 _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 1301 1248 NAG NAG . G 6 NAG A 1 1302 1261 NAG NAG . H 7 CA A 1 1303 1 CA CA . I 7 CA A 1 1304 2 CA CA . J 7 CA A 1 1305 3 CA CA . K 8 EDO A 1 1306 1 EDO EDO . L 8 EDO A 1 1307 2 EDO EDO . M 8 EDO A 1 1308 3 EDO EDO . N 8 EDO A 1 1309 4 EDO EDO . O 8 EDO A 1 1310 5 EDO EDO . P 8 EDO A 1 1311 6 EDO EDO . Q 8 EDO A 1 1312 7 EDO EDO . R 9 HOH A 1 1401 7 HOH HOH . R 9 HOH A 2 1402 5 HOH HOH . R 9 HOH A 3 1403 13 HOH HOH . R 9 HOH A 4 1404 8 HOH HOH . R 9 HOH A 5 1405 9 HOH HOH . R 9 HOH A 6 1406 14 HOH HOH . R 9 HOH A 7 1407 10 HOH HOH . R 9 HOH A 8 1408 12 HOH HOH . R 9 HOH A 9 1409 11 HOH HOH . R 9 HOH A 10 1410 6 HOH HOH . R 9 HOH A 11 1411 4 HOH HOH . R 9 HOH A 12 1412 1 HOH HOH . R 9 HOH A 13 1413 3 HOH HOH . R 9 HOH A 14 1414 2 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 C1 EDO . . . N 8 14.694 -3.71 32.279 1 44.57 ? C1 EDO 1309 A 1 HETATM 2 O O1 EDO . . . N 8 16.124 -3.681 32.178 1 49.47 ? O1 EDO 1309 A 1 HETATM 3 C C2 EDO . . . N 8 14.206 -5.132 32.545 1 45.25 ? C2 EDO 1309 A 1 HETATM 4 O O2 EDO . . . N 8 14.214 -5.896 31.336 1 41.42 ? O2 EDO 1309 A 1 # _model_server_stats.io_time_ms 68 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 316 _model_server_stats.encode_time_ms 22 _model_server_stats.element_count 4 #