data_6EJK # _model_server_result.job_id 3P0aeLV869JrFMfCbbJqbg _model_server_result.datetime_utc '2024-11-04 18:20:44' _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 6ejk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":401}' # _entry.id 6EJK # _exptl.entry_id 6EJK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 605.381 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description Uridine-Diphosphate-Methylene-N-acetyl-galactosamine _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90.27 _cell.angle_gamma 90 _cell.entry_id 6EJK _cell.length_a 60.87 _cell.length_b 126.91 _cell.length_c 71.09 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6EJK _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,E,F 1 1 B,D,G,H 2 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 ? 3 E N N ? 3 G N 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 A2G NDG C1 O1 . O3 HO3 . sing 2 ? 2 3 2 A2G A2G C1 O1 . O4 HO4 . 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 C NDG 1 C 1 NDG A 404 NDG 2 n C A2G 2 C 2 A2G A 403 A2G 2 n C A2G 3 C 3 A2G A 402 A2G 2 n D NDG 1 D 1 NDG B 404 NDG 2 n D A2G 2 D 2 A2G B 403 A2G 2 n D A2G 3 D 3 A2G B 402 A2G # 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 covale ? covale1 A C MSE 1 A MSE 1 1_555 A N MSE 2 A MSE 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.339 ? covale ? covale2 A C MSE 2 A MSE 2 1_555 A N MSE 3 A MSE 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale3 A C MSE 3 A MSE 3 1_555 A N LYS 4 A LYS 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.321 ? covale ? covale4 A C VAL 199 A VAL 199 1_555 A N MSE 200 A MSE 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale5 A C MSE 200 A MSE 200 1_555 A N PHE 201 A PHE 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale6 F O36 BUE . A BUE 405 1_555 C C1 NDG . C NDG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.423 ? covale ? covale7 B C MSE 1 B MSE 1 1_555 B N MSE 2 B MSE 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.314 ? covale ? covale8 B C MSE 2 B MSE 2 1_555 B N MSE 3 B MSE 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? covale ? covale9 B C MSE 3 B MSE 3 1_555 B N LYS 4 B LYS 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.316 ? covale ? covale10 B C VAL 199 B VAL 199 1_555 B N MSE 200 B MSE 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale11 B C MSE 200 B MSE 200 1_555 B N PHE 201 B PHE 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale12 H O36 BUE . B BUE 405 1_555 D C1 NDG . D NDG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.418 ? covale ? covale13 C O3 NDG . C NDG 1 1_555 C C1 A2G . C A2G 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.373 ? covale ? covale14 C O4 A2G . C A2G 2 1_555 C C1 A2G . C A2G 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.423 ? covale ? covale15 D O3 NDG . D NDG 1 1_555 D C1 A2G . D A2G 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.371 ? covale ? covale16 D O4 A2G . D A2G 2 1_555 D C1 A2G . D A2G 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.413 ? # _chem_comp.formula 'C18 H29 N3 O16 P2' _chem_comp.formula_weight 605.381 _chem_comp.id UDN _chem_comp.mon_nstd_flag . _chem_comp.name Uridine-Diphosphate-Methylene-N-acetyl-galactosamine _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 O4 C4 UDN doub 480 n n N3 C4 UDN sing 481 n n N3 C2 UDN sing 482 n n C4 C5 UDN sing 483 n n O2 C2 UDN doub 484 n n C2 N1 UDN sing 485 n n O2' C2D UDN sing 486 n n C5 C6 UDN doub 487 n n N1 C6 UDN sing 488 n n N1 C1D UDN sing 489 n n C2D C1D UDN sing 490 n n C2D C3D UDN sing 491 n n C1D O4D UDN sing 492 n n C3D O3D UDN sing 493 n n C3D C4D UDN sing 494 n n O4D C4D UDN sing 495 n n C4D C5D UDN sing 496 n n C5D O5D UDN sing 497 n n O5D PA UDN sing 498 n n O2A PA UDN doub 499 n n PA O1A UDN sing 500 n n PA O3A UDN sing 501 n n O3A PB UDN sing 502 n n PB O1B UDN doub 503 n n PB O2B UDN sing 504 n n PB CB UDN sing 505 n n C6' C5' UDN sing 506 n n C6' O6' UDN sing 507 n n CB C1' UDN sing 508 n n C5' O5' UDN sing 509 n n C5' C4' UDN sing 510 n n O5' C1' UDN sing 511 n n C1' C2' UDN sing 512 n n C4' C3' UDN sing 513 n n C4' O4' UDN sing 514 n n C3' C2' UDN sing 515 n n C3' O3' UDN sing 516 n n C2' N2' UDN sing 517 n n N2' C7' UDN sing 518 n n C7' C8' UDN sing 519 n n C7' O7' UDN doub 520 n n C1' H1 UDN sing 521 n n C2' H2 UDN sing 522 n n C3' H3 UDN sing 523 n n C4' H4 UDN sing 524 n n C5' H5 UDN sing 525 n n C6' H6 UDN sing 526 n n C6' H7 UDN sing 527 n n C8' H8 UDN sing 528 n n C8' H9 UDN sing 529 n n C8' H10 UDN sing 530 n n N2' H11 UDN sing 531 n n CB H12 UDN sing 532 n n CB H13 UDN sing 533 n n O3' H14 UDN sing 534 n n O4' H15 UDN sing 535 n n O6' H16 UDN sing 536 n n N3 H17 UDN sing 537 n n C5 H18 UDN sing 538 n n C6 H19 UDN sing 539 n n C1D H20 UDN sing 540 n n C2D H21 UDN sing 541 n n O2' H22 UDN sing 542 n n C3D H23 UDN sing 543 n n C4D H24 UDN sing 544 n n O3D H25 UDN sing 545 n n C5D H26 UDN sing 546 n n C5D H27 UDN sing 547 n n O1A H28 UDN sing 548 n n O2B H29 UDN sing 549 n n # _atom_sites.entry_id 6EJK _atom_sites.fract_transf_matrix[1][1] 0.016428 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000076 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.00788 _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] 0.014067 _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 E 3 UDN A 1 401 401 UDN UDN . F 4 BUE A 1 405 405 BUE BUE . G 3 UDN B 1 401 401 UDN UDN . H 4 BUE B 1 405 405 BUE BUE . # 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' UDN . . . E 3 68.818 -6.57 22.468 1 89.74 ? C1' UDN 401 A 1 HETATM 2 C C2' UDN . . . E 3 68.209 -5.684 23.543 1 91.34 ? C2' UDN 401 A 1 HETATM 3 C C3' UDN . . . E 3 68.13 -4.254 23.035 1 90.41 ? C3' UDN 401 A 1 HETATM 4 C C4' UDN . . . E 3 69.442 -3.685 22.55 1 89.67 ? C4' UDN 401 A 1 HETATM 5 C C5' UDN . . . E 3 70.131 -4.636 21.585 1 88.05 ? C5' UDN 401 A 1 HETATM 6 C C6' UDN . . . E 3 71.497 -4.168 21.234 1 87.68 ? C6' UDN 401 A 1 HETATM 7 C C7' UDN . . . E 3 66.4 -6.46 25.246 1 94.55 ? C7' UDN 401 A 1 HETATM 8 C C8' UDN . . . E 3 65.005 -7.057 25.427 1 95.15 ? C8' UDN 401 A 1 HETATM 9 N N2' UDN . . . E 3 66.863 -6.263 23.886 1 92.05 ? N2' UDN 401 A 1 HETATM 10 C CB UDN . . . E 3 67.916 -6.596 21.41 1 88.15 ? CB UDN 401 A 1 HETATM 11 O O3' UDN . . . E 3 67.514 -3.38 24.003 1 92.31 ? O3' UDN 401 A 1 HETATM 12 O O4' UDN . . . E 3 70.331 -3.413 23.636 1 91.91 ? O4' UDN 401 A 1 HETATM 13 O O5' UDN . . . E 3 70.161 -6.057 22.097 1 89.12 ? O5' UDN 401 A 1 HETATM 14 O O6' UDN . . . E 3 72.408 -4.668 22.195 1 89.67 ? O6' UDN 401 A 1 HETATM 15 O O7' UDN . . . E 3 67.054 -6.168 26.205 1 96.39 ? O7' UDN 401 A 1 HETATM 16 N N1 UDN . . . E 3 66.822 -10.099 12.667 1 84.54 ? N1 UDN 401 A 1 HETATM 17 C C2 UDN . . . E 3 67.404 -10.864 11.687 1 85.08 ? C2 UDN 401 A 1 HETATM 18 N N3 UDN . . . E 3 66.66 -11.786 11.056 1 86.99 ? N3 UDN 401 A 1 HETATM 19 C C4 UDN . . . E 3 65.376 -11.966 11.361 1 88.26 ? C4 UDN 401 A 1 HETATM 20 C C5 UDN . . . E 3 64.769 -11.204 12.356 1 87.54 ? C5 UDN 401 A 1 HETATM 21 C C6 UDN . . . E 3 65.543 -10.261 13.009 1 85.68 ? C6 UDN 401 A 1 HETATM 22 O O2 UDN . . . E 3 68.565 -10.711 11.385 1 84.17 ? O2 UDN 401 A 1 HETATM 23 O O4 UDN . . . E 3 64.718 -12.787 10.777 1 90.33 ? O4 UDN 401 A 1 HETATM 24 C C1D UDN . . . E 3 67.607 -9.075 13.39 1 83.06 ? C1D UDN 401 A 1 HETATM 25 C C2D UDN . . . E 3 67.664 -7.685 13.066 1 81.68 ? C2D UDN 401 A 1 HETATM 26 O O2' UDN . . . E 3 68.174 -7.154 11.908 1 80.7 ? O2' UDN 401 A 1 HETATM 27 C C3D UDN . . . E 3 67.95 -7.049 14.261 1 81.5 ? C3D UDN 401 A 1 HETATM 28 C C4D UDN . . . E 3 67.456 -7.986 15.384 1 82.83 ? C4D UDN 401 A 1 HETATM 29 O O4D UDN . . . E 3 67.86 -9.232 14.65 1 83.55 ? O4D UDN 401 A 1 HETATM 30 O O3D UDN . . . E 3 68.963 -6.027 14.273 1 80.46 ? O3D UDN 401 A 1 HETATM 31 C C5D UDN . . . E 3 67.726 -7.742 16.593 1 83.7 ? C5D UDN 401 A 1 HETATM 32 O O5D UDN . . . E 3 67.606 -6.501 16.859 1 83.04 ? O5D UDN 401 A 1 HETATM 33 P PA UDN . . . E 3 67.05 -6.147 18.362 1 84.47 ? PA UDN 401 A 1 HETATM 34 O O1A UDN . . . E 3 67.751 -4.978 18.921 1 84.53 ? O1A UDN 401 A 1 HETATM 35 O O2A UDN . . . E 3 65.607 -5.832 18.334 1 84.96 ? O2A UDN 401 A 1 HETATM 36 O O3A UDN . . . E 3 67.309 -7.659 19.056 1 85.82 ? O3A UDN 401 A 1 HETATM 37 P PB UDN . . . E 3 67.27 -7.962 20.683 1 87.89 ? PB UDN 401 A 1 HETATM 38 O O1B UDN . . . E 3 68.011 -9.18 20.909 1 88.89 ? O1B UDN 401 A 1 HETATM 39 O O2B UDN . . . E 3 65.956 -8.323 21.197 1 89.07 ? O2B UDN 401 A 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 35 _model_server_stats.query_time_ms 319 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 39 #